## [1] "Available PharmacoSets"
## [1] "GDSC_2020(v2-8.2)" "FIMM_2016" "Tavor_2020"
## [4] "NCI60_2021" "UHNBreast_2019" "GDSC_2020(v1-8.2)"
## [7] "PRISM_2020" "BeatAML_2018" "gCSI_2019"
## [10] "CTRPv2_2015" "GRAY_2017" "CCLE_2015"
## [13] "PDTX_2019" "GBM_scr2" "GBM_scr3"## Reading in oldGDSC
## Reading in oldCCLE
## Reading in oldgCSI## Reading in new GDSC
## Reading in new CCLE
## Reading in new gCSI## <PharmacoSet>
## Name: CCLE_(2019)
## Date Created: Fri Apr 19 18:36:32 2024
## Number of samples: 1457
## Molecular profiles:
## A MultiAssayExperiment object of 6 listed
## experiments with user-defined names and respective classes.
## Containing an ExperimentList class object of length 6:
## [1] rnaseq.transcripts_tpm: RangedSummarizedExperiment with 57820 rows and 1018 columns
## [2] rnaseq.genes_tpm: RangedSummarizedExperiment with 196520 rows and 1018 columns
## [3] rnaseq.genes_counts: RangedSummarizedExperiment with 56202 rows and 1018 columns
## [4] rnaseq.genes_rpkm: RangedSummarizedExperiment with 56202 rows and 1018 columns
## [5] cnv.genes: RangedSummarizedExperiment with 23316 rows and 993 columns
## [6] mut.genes: RangedSummarizedExperiment with 1667 rows and 920 columns
## Treatment response:
## <TreatmentResponseExperiment>
## dim: 184 493
## assays(2): sensitivity profiles
## rownames(184): 17AAG:0.0025 17AAG:0.008 ... TOPOTECAN:2.53 TOPOTECAN:8
## rowData(2): treatmentid dose
## colnames(493): 1321N1 22Rv1 42-MG-BA ... YKG-1 ZR-75-1 ZR-75-30
## colData(1): sampleid
## metadata(5): data_source filename annotation date sessionInfo## <PharmacoSet>
## Name: CCLE
## Date Created: Tue Jun 23 22:46:09 2020
## Number of samples: 1094
## Molecular profiles:
## RNA :
## Dim: 20024, 1036
## Kallisto_0.46.1.rnaseq :
## Dim: 60662, 1019
## Kallisto_0.46.1.rnaseq.counts :
## Dim: 60662, 1019
## Kallisto_0.46.1.isoforms :
## Dim: 227912, 1019
## Kallisto_0.46.1.isoforms.counts :
## Dim: 227912, 1019
## mutation :
## Dim: 1667, 1053
## CNV :
## Dim: 22907, 945
## Treatment response:
## Drug pertubation:
## Please look at pertNumber(cSet) to determine number of experiments for each drug-sample combination.
## Drug sensitivity:
## Number of Experiments: 11670
## Please look at sensNumber(cSet) to determine number of experiments for each drug-sample combination.Old Sample Info
## --------------------------------------------------------------------------------
## Old Treatment Info
## --------------------------------------------------------------------------------
## Num Samples in Old Treatment Info: 24
## [1] "Treatment Info Columns"
## [1] "Compound..code.or.generic.name." "Compound..brand.name."
## [3] "Target.s." "Mechanism.of.action"
## [5] "Class" "Highest.Phase"
## [7] "Organization" "Compound"
## [9] "treatmentid" "drug.name"
## [11] "smiles" "inchikey"
## [13] "cid" "FDA"New Sample Info
## --------------------------------------------------------------------------------
## New Treatment Info
## --------------------------------------------------------------------------------
## Num Samples in New Treatment Info: 24
## [1] "Treatment Info Columns"
## [1] "CCLE.treatmentid" "CCLE.raw_treatmentid"
## [3] "CCLE.target" "CCLE.mechanismOfAction"
## [5] "CCLE.class" "CCLE.highestClinicalTrialPhase"
## [7] "CCLE.treatmentSourceOrganization" "unichem.ChEMBL"
## [9] "pubchem.CID" "pubchem.MolecularFormula"
## [11] "pubchem.CanonicalSMILES" "pubchem.InChIKey"
## [13] "pubchem.Title" "unichem.ChEBI"
## [15] "unichem.clinicaltrials" "unichem.DrugBank"
## [17] "unichem.FDA_SRS" "unichem.LINCS"
## [19] "unichem.PharmGKB" "unichem.rxnorm"
## [21] "chembl.parent_molecule_chembl_id" "chembl.target_chembl_id"
## [23] "chembl.record_id" "chembl.mechanism_of_action"
## [25] "chembl.mechanism_comment" "chembl.action_type"
## [27] "treatmentid" "unique.treatmentid"Old Treatment Info
## --------------------------------------------------------------------------------
## Old Treatment Info
## --------------------------------------------------------------------------------
## Num Samples in Old Treatment Info: 24
## [1] "Treatment Info Columns"
## [1] "Compound..code.or.generic.name." "Compound..brand.name."
## [3] "Target.s." "Mechanism.of.action"
## [5] "Class" "Highest.Phase"
## [7] "Organization" "Compound"
## [9] "treatmentid" "drug.name"
## [11] "smiles" "inchikey"
## [13] "cid" "FDA"New Treatment Info
## --------------------------------------------------------------------------------
## New Treatment Info
## --------------------------------------------------------------------------------
## Num Samples in New Treatment Info: 24
## [1] "Treatment Info Columns"
## [1] "CCLE.treatmentid" "CCLE.raw_treatmentid"
## [3] "CCLE.target" "CCLE.mechanismOfAction"
## [5] "CCLE.class" "CCLE.highestClinicalTrialPhase"
## [7] "CCLE.treatmentSourceOrganization" "unichem.ChEMBL"
## [9] "pubchem.CID" "pubchem.MolecularFormula"
## [11] "pubchem.CanonicalSMILES" "pubchem.InChIKey"
## [13] "pubchem.Title" "unichem.ChEBI"
## [15] "unichem.clinicaltrials" "unichem.DrugBank"
## [17] "unichem.FDA_SRS" "unichem.LINCS"
## [19] "unichem.PharmGKB" "unichem.rxnorm"
## [21] "chembl.parent_molecule_chembl_id" "chembl.target_chembl_id"
## [23] "chembl.record_id" "chembl.mechanism_of_action"
## [25] "chembl.mechanism_comment" "chembl.action_type"
## [27] "treatmentid" "unique.treatmentid"## --------------------------------------------------------------------------------
## Old Molecular Profiles with Annotation: microarray/rna
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: rna
## [1] "Assay Names: exprs"
## [1] "Num Samples: 20024"
## [1] "Num Features: 1036"
## [1] "No Description"
## --------------------------------------------------------------------------------
## New Molecular Profiles with Annotation: microarray/rna
## --------------------------------------------------------------------------------
## No new molecular profiles with annotationfor the OLD CCLE RNASeq data, the data is
transformed as follows: based on the orcestra
page for CCLE -
Gene TPM Values: After estimation by the tool detailed above, gene TPM values are transformed by log2(x + 0.001).
-
Gene Count Values: After estimation by the tool detailed above, gene count values are transformed by log2(x + 1).
## --------------------------------------------------------------------------------
## Old Molecular Profiles with Annotation: rnaseq
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: Kallisto_0.46.1.rnaseq
## [1] "Assay Names: exprs"
## [1] "Num Samples: 60662"
## [1] "Num Features: 1019"
## [1] "No Description"
## SummarizedExperiment Name: Kallisto_0.46.1.rnaseq.counts
## [1] "Assay Names: exprs"
## [1] "Num Samples: 60662"
## [1] "Num Features: 1019"
## [1] "No Description"
## --------------------------------------------------------------------------------
## New Molecular Profiles with Annotation: rnaseq
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: rnaseq.transcripts_tpm
## [1] "Assay Names: exprs"
## [1] "Num Samples: 57820"
## [1] "Num Features: 1018"
## [1] "Source Description: Read counts, TPM & FPKM-values for all sequenced models including cell lines and organoids."
## SummarizedExperiment Name: rnaseq.genes_tpm
## [1] "Assay Names: exprs"
## [1] "Num Samples: 196520"
## [1] "Num Features: 1018"
## [1] "Source Description: Read counts, TPM & FPKM-values for all sequenced models including cell lines and organoids."
## SummarizedExperiment Name: rnaseq.genes_counts
## [1] "Assay Names: exprs"
## [1] "Num Samples: 56202"
## [1] "Num Features: 1018"
## [1] "Source Description: Read counts, TPM & FPKM-values for all sequenced models including cell lines and organoids."
## SummarizedExperiment Name: rnaseq.genes_rpkm
## [1] "Assay Names: exprs"
## [1] "Num Samples: 56202"
## [1] "Num Features: 1018"
## [1] "Source Description: Read counts, TPM & FPKM-values for all sequenced models including cell lines and organoids."## --------------------------------------------------------------------------------
## Old Molecular Profiles with Annotation: cnv
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: cnv
## [1] "Assay Names: exprs"
## [1] "Num Samples: 22907"
## [1] "Num Features: 945"
## [1] "No Description"
## --------------------------------------------------------------------------------
## New Molecular Profiles with Annotation: cnv
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: cnv.genes
## [1] "Assay Names: exprs"
## [1] "Num Samples: 23316"
## [1] "Num Features: 993"
## [1] "Source Description: "## --------------------------------------------------------------------------------
## Old Molecular Profiles with Annotation: mutation/mut
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: mutation
## [1] "Assay Names: exprs"
## [1] "Num Samples: 1667"
## [1] "Num Features: 1053"
## [1] "No Description"
## --------------------------------------------------------------------------------
## New Molecular Profiles with Annotation: mutation/mut
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: mut.genes
## [1] "Assay Names: exprs"
## [1] "Num Samples: 1667"
## [1] "Num Features: 920"
## [1] "Source Description: TODO::(add description)"## --------------------------------------------------------------------------------
## Old Treatment Response
## --------------------------------------------------------------------------------
## Old Treatment Response is a list of DataFrames
## [1] "Number of treatments: 24"
## [1] "Number of samples: 503"
## [1] "Total number of experiments: 11670"
## [1] "Profiles DataFrame: "
## ic50_published aac_published amax_published
## drugid_AEW541_1321N1 262 0.0873750 164
## drugid_AEW541_22Rv1 78 0.2205000 361
## drugid_AEW541_42-MG-BA 90 0.1144375 309
## drugid_AEW541_5637 173 0.1243550 300
## drugid_AEW541_639-V 59 0.1936250 234
## drugid_AEW541_697 149 0.1087625 367
## aac_recomputed ic50_recomputed HS E_inf
## drugid_AEW541_1321N1 0.09800818 16.332263 0.9169196 38.47711
## drugid_AEW541_22Rv1 0.21323823 2.034710 0.8374151 13.95620
## drugid_AEW541_42-MG-BA 0.12151155 2.687672 2.9099240 36.28378
## drugid_AEW541_5637 0.10877695 5.192732 1.0883419 0.00000
## drugid_AEW541_639-V 0.18344576 5.113119 0.6991911 30.29307
## drugid_AEW541_697 0.10518547 4.254253 1.5039911 0.00000
## EC50
## drugid_AEW541_1321N1 3.295213
## drugid_AEW541_22Rv1 1.376470
## drugid_AEW541_42-MG-BA 1.723197
## drugid_AEW541_5637 5.192732
## drugid_AEW541_639-V 1.350123
## drugid_AEW541_697 4.254253
## --------------------------------------------------------------------------------
## New Treatment Response
## --------------------------------------------------------------------------------
## New Treatment Response is a TreatmentResponseExperiment
## [1] "Number of treatments: 23"
## [1] "Number of samples: 493"
## [1] "Total number of experiments: 87308"
## [1] "Profiles/Summary Assay: "
## Key: <treatmentid, sampleid>
## treatmentid sampleid HS E_inf EC50 Rsq
## <char> <char> <num> <num> <num> <num>
## 1: 17AAG 1321N1 1.0000000 27.000000 0.00250000 -0.04905813
## 2: 17AAG 22Rv1 1.4100034 20.112878 0.24562282 0.97167493
## 3: 17AAG 42-MG-BA 0.5788574 9.487915 0.02413061 0.69470957
## 4: 17AAG 5637 1.0000000 8.000000 0.08000000 0.93019991
## 5: 17AAG 639V 2.2293532 9.995242 0.12816153 0.97932740
## 6: 17AAG 697 1.0000000 8.000000 0.25000000 0.90021928
## aac_recomputed ic50_recomputed published_EC50 published_IC50 published_Amax
## <num> <num> <num> <num> <num>
## 1: 66.73343 0.005434783 0.19367672 0.22807844 -72.12381
## 2: 34.51985 0.353809081 0.26721454 0.32970169 -76.30148
## 3: 61.13015 0.034708865 0.05208059 0.05303809 -80.37766
## 4: 52.25685 0.095238095 0.06090715 0.07082279 -91.65148
## 5: 46.10002 0.141646073 0.14792989 0.15009449 -89.63907
## 6: 39.74315 0.297619048 0.37833494 0.42257124 -91.79781
## published_ActArea
## <num>
## 1: 3.0302
## 2: 3.0622
## 3: 5.0587
## 4: 3.5350
## 5: 3.7820
## 6: 3.6605## <PharmacoSet>
## Name: GDSC2v8.4
## Date Created: Fri Apr 19 16:58:53 2024
## Number of samples: 1000
## Molecular profiles:
## A MultiAssayExperiment object of 15 listed
## experiments with user-defined names and respective classes.
## Containing an ExperimentList class object of length 15:
## [1] rnaseq.fpkm: RangedSummarizedExperiment with 37313 rows and 949 columns
## [2] rnaseq.read_count: RangedSummarizedExperiment with 37313 rows and 949 columns
## [3] rnaseq.tpm: RangedSummarizedExperiment with 37313 rows and 949 columns
## [4] cnv.total_copy_number: RangedSummarizedExperiment with 18319 rows and 934 columns
## [5] cnv.cn_category: RangedSummarizedExperiment with 18319 rows and 934 columns
## [6] cnv.seg_mean: RangedSummarizedExperiment with 18319 rows and 934 columns
## [7] cnv.gene_mean: RangedSummarizedExperiment with 18319 rows and 934 columns
## [8] cnv.num_snps: RangedSummarizedExperiment with 18319 rows and 934 columns
## [9] cnv.gatk_mean_log2_copy_ratio: RangedSummarizedExperiment with 18319 rows and 934 columns
## [10] mut.protein: RangedSummarizedExperiment with 19925 rows and 935 columns
## [11] mut.rna: RangedSummarizedExperiment with 19925 rows and 935 columns
## [12] mut.cdna: RangedSummarizedExperiment with 19925 rows and 935 columns
## [13] mut.vaf: RangedSummarizedExperiment with 19925 rows and 935 columns
## [14] mut.effect: RangedSummarizedExperiment with 19925 rows and 935 columns
## [15] fusion: SummarizedExperiment with 6219 rows and 874 columns
## Treatment response:
## <TreatmentResponseExperiment>
## dim: 362 1665
## assays(3): sensitivity profiles_published profiles
## rownames(362): AFATINIB:0.00200105397013264 AFATINIB:0.00400210794026528 ... VORINOSTAT:5 VORINOSTAT:10
## rowData(2): treatmentid Dose
## colnames(1665): 697:5164 697:5424 697:9676 ... YKG-1:43605 YKG-1:43606 YKG-1:43607
## colData(2): sampleid BARCODE
## metadata(3): data_source filename date## <PharmacoSet>
## Name: GDSC_v2
## Date Created: Thu Dec 16 20:04:13 2021
## Number of samples: 1084
## Molecular profiles:
## Kallisto_0.46.1.rnaseq :
## Dim: 60662, 462
## Kallisto_0.46.1.rnaseq.counts :
## Dim: 60662, 462
## Kallisto_0.46.1.isoforms :
## Dim: 227912, 462
## Kallisto_0.46.1.isoforms.counts :
## Dim: 227912, 462
## RNA :
## Dim: 17611, 1018
## mutation :
## Dim: 67, 707
## mutation_exome :
## Dim: 278, 941
## fusion :
## Dim: 3, 707
## CNV :
## Dim: 22902, 968
## Treatment response:
## Drug pertubation:
## Please look at pertNumber(cSet) to determine number of experiments for each drug-sample combination.
## Drug sensitivity:
## Number of Experiments: 215780
## Please look at sensNumber(cSet) to determine number of experiments for each drug-sample combination.Old Sample Info
## --------------------------------------------------------------------------------
## Old Sample Info
## --------------------------------------------------------------------------------
## Num Samples in Old: 1084
## [1] "Sample Info Columns"
## [1] "Sample.Name"
## [2] "COSMIC.identifier"
## [3] "Whole.Exome.Sequencing..WES."
## [4] "Copy.Number.Alterations..CNA."
## [5] "Gene.Expression"
## [6] "Methylation"
## [7] "Drug..Response"
## [8] "GDSC..Tissue.descriptor.1"
## [9] "GDSC..Tissue..descriptor.2"
## [10] "Cancer.Type...matching.TCGA.label."
## [11] "Microsatellite...instability.Status..MSI."
## [12] "Screen.Medium"
## [13] "Growth.Properties"
## [14] "sampleid"
## [15] "tissueid"
## [16] "Cellosaurus.Disease.Type"
## [17] "Cellosaurus.Accession.id"
## [18] "PharmacoDB.id"
## [19] "unique.tissueid.fromstudies"
## [20] "CellLine.Type"
## [21] "Metastatic"New Sample Info
## --------------------------------------------------------------------------------
## New Sample Info
## --------------------------------------------------------------------------------
## Num Samples in New: 1000
## [1] "Sample Info Columns"
## [1] "cellosaurus.accession"
## [2] "cellosaurus.cellLineName"
## [3] "cellosaurus.category"
## [4] "cellosaurus.date"
## [5] "cellosaurus.ageAtSampling"
## [6] "cellosaurus.sexOfCell"
## [7] "cellosaurus.synonyms"
## [8] "cellosaurus.diseases"
## [9] "GDSC.sampleid"
## [10] "GDSC.Sample_Name"
## [11] "CCLE.sampleid"
## [12] "GDSC.BROAD_ID"
## [13] "GDSC.RRID"
## [14] "CMP.model_id"
## [15] "CMP.sampleid"
## [16] "GDSC.COSMIC_ID"
## [17] "GDSC.Whole_Exome_Sequencing_.WES."
## [18] "GDSC.Copy_Number_Alterations_.CNA."
## [19] "GDSC.Gene_Expression"
## [20] "GDSC.Methylation"
## [21] "GDSC.DrugResponse"
## [22] "GDSC.Tissue_descriptor_1"
## [23] "GDSC.Tissuedescriptor_2"
## [24] "GDSC.Cancer_Type.matching_TCGA_label."
## [25] "GDSC.Microsatellite_instability_Status_.MSI."
## [26] "GDSC.Screen_Medium"
## [27] "GDSC.Growth_Properties"
## [28] "GDSC.tissue"
## [29] "GDSC.cancer_type"
## [30] "GDSC.cancer_type_ncit_id"
## [31] "GDSC.sample_site"
## [32] "GDSC.gender"
## [33] "GDSC.ethnicity"
## [34] "GDSC.age_at_sampling"
## [35] "sampleid"Old Treatment Info
## --------------------------------------------------------------------------------
## Old Treatment Info
## --------------------------------------------------------------------------------
## Num Samples in Old Treatment Info: 190
## [1] "Treatment Info Columns"
## [1] "DRUG_ID" "SCREENING_SITE" "DRUG_NAME" "SYNONYMS"
## [5] "TARGET" "TARGET_PATHWAY" "treatmentid" "smiles"
## [9] "inchikey" "cid" "FDA"New Treatment Info
## --------------------------------------------------------------------------------
## New Treatment Info
## --------------------------------------------------------------------------------
## Num Samples in New Treatment Info: 538
## [1] "Treatment Info Columns"
## [1] "pubchem.CID" "GDSC.treatmentid"
## [3] "GDSC.DRUG_ID" "GDSC.SCREENING_SITE"
## [5] "GDSC.DRUG_NAME" "GDSC.SYNONYMS"
## [7] "GDSC.TARGET" "GDSC.TARGET_PATHWAY"
## [9] "pubchem.MolecularFormula" "pubchem.CanonicalSMILES"
## [11] "pubchem.InChIKey" "pubchem.Title"
## [13] "treatmentid" "unichem.ChEMBL"
## [15] "unichem.ChEBI" "unichem.DrugBank"
## [17] "unichem.LINCS" "unichem.FDA_SRS"
## [19] "unichem.clinicaltrials" "unichem.PharmGKB"
## [21] "unichem.rxnorm" "unichem.NIH_Clinical_Collection"## --------------------------------------------------------------------------------
## Old Molecular Profiles with Annotation: microarray/rna
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: rna
## [1] "Assay Names: exprs, se.exprs"
## [1] "Num Samples: 17611"
## [1] "Num Features: 1018"
## [1] "No Description"
## --------------------------------------------------------------------------------
## New Molecular Profiles with Annotation: microarray/rna
## --------------------------------------------------------------------------------
## No new molecular profiles with annotationfor the OLD GDSC RNASeq data, the data is
transformed as follows: based on the orcestra
page for GDSC -
Gene TPM Values: After estimation by the tool detailed above, gene TPM values are transformed by log2(x + 0.001).
-
Gene Count Values: After estimation by the tool detailed above, gene count values are transformed by log2(x + 1).
## --------------------------------------------------------------------------------
## Old Molecular Profiles with Annotation: rnaseq
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: Kallisto_0.46.1.rnaseq
## [1] "Assay Names: exprs"
## [1] "Num Samples: 60662"
## [1] "Num Features: 462"
## [1] "No Description"
## SummarizedExperiment Name: Kallisto_0.46.1.rnaseq.counts
## [1] "Assay Names: exprs"
## [1] "Num Samples: 60662"
## [1] "Num Features: 462"
## [1] "No Description"
## --------------------------------------------------------------------------------
## New Molecular Profiles with Annotation: rnaseq
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: rnaseq.fpkm
## [1] "Assay Names: exprs"
## [1] "Num Samples: 37313"
## [1] "Num Features: 949"
## [1] "Source Description: Read counts, TPM & FPKM-values for all sequenced models including cell lines and organoids."
## SummarizedExperiment Name: rnaseq.read_count
## [1] "Assay Names: exprs"
## [1] "Num Samples: 37313"
## [1] "Num Features: 949"
## [1] "Source Description: Read counts, TPM & FPKM-values for all sequenced models including cell lines and organoids."
## SummarizedExperiment Name: rnaseq.tpm
## [1] "Assay Names: exprs"
## [1] "Num Samples: 37313"
## [1] "Num Features: 949"
## [1] "Source Description: Read counts, TPM & FPKM-values for all sequenced models including cell lines and organoids."## --------------------------------------------------------------------------------
## Old Molecular Profiles with Annotation: cnv
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: cnv
## [1] "Assay Names: exprs"
## [1] "Num Samples: 22902"
## [1] "Num Features: 968"
## [1] "No Description"
## --------------------------------------------------------------------------------
## New Molecular Profiles with Annotation: cnv
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: cnv.total_copy_number
## [1] "Assay Names: exprs"
## [1] "Num Samples: 18319"
## [1] "Num Features: 934"
## [1] "Source Description: "
## SummarizedExperiment Name: cnv.cn_category
## [1] "Assay Names: exprs"
## [1] "Num Samples: 18319"
## [1] "Num Features: 934"
## [1] "Source Description: "
## SummarizedExperiment Name: cnv.seg_mean
## [1] "Assay Names: exprs"
## [1] "Num Samples: 18319"
## [1] "Num Features: 934"
## [1] "Source Description: "
## SummarizedExperiment Name: cnv.gene_mean
## [1] "Assay Names: exprs"
## [1] "Num Samples: 18319"
## [1] "Num Features: 934"
## [1] "Source Description: "
## SummarizedExperiment Name: cnv.num_snps
## [1] "Assay Names: exprs"
## [1] "Num Samples: 18319"
## [1] "Num Features: 934"
## [1] "Source Description: "
## SummarizedExperiment Name: cnv.gatk_mean_log2_copy_ratio
## [1] "Assay Names: exprs"
## [1] "Num Samples: 18319"
## [1] "Num Features: 934"
## [1] "Source Description: "## --------------------------------------------------------------------------------
## Old Molecular Profiles with Annotation: mutation/mut
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: mutation
## [1] "Assay Names: exprs"
## [1] "Num Samples: 67"
## [1] "Num Features: 707"
## [1] "No Description"
## SummarizedExperiment Name: mutation_exome
## [1] "Assay Names: exprs"
## [1] "Num Samples: 278"
## [1] "Num Features: 941"
## [1] "No Description"
## --------------------------------------------------------------------------------
## New Molecular Profiles with Annotation: mutation/mut
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: mut.protein
## [1] "Assay Names: exprs"
## [1] "Num Samples: 19925"
## [1] "Num Features: 935"
## [1] "Source Description: A list of all mutations present in all sequenced models."
## SummarizedExperiment Name: mut.rna
## [1] "Assay Names: exprs"
## [1] "Num Samples: 19925"
## [1] "Num Features: 935"
## [1] "Source Description: A list of all mutations present in all sequenced models."
## SummarizedExperiment Name: mut.cdna
## [1] "Assay Names: exprs"
## [1] "Num Samples: 19925"
## [1] "Num Features: 935"
## [1] "Source Description: A list of all mutations present in all sequenced models."
## SummarizedExperiment Name: mut.vaf
## [1] "Assay Names: exprs"
## [1] "Num Samples: 19925"
## [1] "Num Features: 935"
## [1] "Source Description: A list of all mutations present in all sequenced models."
## SummarizedExperiment Name: mut.effect
## [1] "Assay Names: exprs"
## [1] "Num Samples: 19925"
## [1] "Num Features: 935"
## [1] "Source Description: A list of all mutations present in all sequenced models."## --------------------------------------------------------------------------------
## Old Treatment Response
## --------------------------------------------------------------------------------
## Old Treatment Response is a list of DataFrames
## [1] "Number of treatments: 190"
## [1] "Number of samples: 809"
## [1] "Total number of experiments: 215780"
## [1] "Profiles DataFrame: "
## aac_recomputed
## PC-14_Camptothecin_1003_3230_SeedDens_250_assay_Glo_dur_4 0.115669207
## PC-14_PD-0325901_1060_3230_SeedDens_250_assay_Glo_dur_4 0.055431877
## PC-14_Entinostat_1593_3230_SeedDens_250_assay_Glo_dur_4 0.169286153
## PC-14_VE-822_1613_3230_SeedDens_250_assay_Glo_dur_4 0.033331791
## PC-14_WZ4003_1614_3230_SeedDens_250_assay_Glo_dur_4 0.055152910
## PC-14_CZC24832_1615_3230_SeedDens_250_assay_Glo_dur_4 0.009643103
## ic50_recomputed
## PC-14_Camptothecin_1003_3230_SeedDens_250_assay_Glo_dur_4 0.1521703
## PC-14_PD-0325901_1060_3230_SeedDens_250_assay_Glo_dur_4 NA
## PC-14_Entinostat_1593_3230_SeedDens_250_assay_Glo_dur_4 NA
## PC-14_VE-822_1613_3230_SeedDens_250_assay_Glo_dur_4 4.5093150
## PC-14_WZ4003_1614_3230_SeedDens_250_assay_Glo_dur_4 NA
## PC-14_CZC24832_1615_3230_SeedDens_250_assay_Glo_dur_4 NA
## HS E_inf
## PC-14_Camptothecin_1003_3230_SeedDens_250_assay_Glo_dur_4 1.520145 47.03493
## PC-14_PD-0325901_1060_3230_SeedDens_250_assay_Glo_dur_4 4.000000 84.90308
## PC-14_Entinostat_1593_3230_SeedDens_250_assay_Glo_dur_4 4.000000 54.47200
## PC-14_VE-822_1613_3230_SeedDens_250_assay_Glo_dur_4 4.000000 0.00000
## PC-14_WZ4003_1614_3230_SeedDens_250_assay_Glo_dur_4 4.000000 59.48966
## PC-14_CZC24832_1615_3230_SeedDens_250_assay_Glo_dur_4 4.000000 61.56250
## EC50
## PC-14_Camptothecin_1003_3230_SeedDens_250_assay_Glo_dur_4 0.02372539
## PC-14_PD-0325901_1060_3230_SeedDens_250_assay_Glo_dur_4 0.01979284
## PC-14_Entinostat_1593_3230_SeedDens_250_assay_Glo_dur_4 0.76665986
## PC-14_VE-822_1613_3230_SeedDens_250_assay_Glo_dur_4 4.50931499
## PC-14_WZ4003_1614_3230_SeedDens_250_assay_Glo_dur_4 3.92779893
## PC-14_CZC24832_1615_3230_SeedDens_250_assay_Glo_dur_4 10.00000000
## --------------------------------------------------------------------------------
## New Treatment Response
## --------------------------------------------------------------------------------
## New Treatment Response is a TreatmentResponseExperiment
## [1] "Number of treatments: 30"
## [1] "Number of samples: 100"
## [1] "Total number of experiments: 51681"
## [1] "Profiles/Summary Assay: "
## Key: <treatmentid, sampleid>
## treatmentid sampleid HS E_inf EC50 Rsq
## <char> <char> <num> <num> <num> <num>
## 1: AFATINIB 697 1.0000000 0.02838418 2.00000000 0.8840460
## 2: AFATINIB A4-FUK 1.0000000 0.04875089 2.00000000 0.7984359
## 3: AFATINIB A431 0.2541719 0.00000000 0.39857465 0.5502951
## 4: AFATINIB ASPC-1 1.0000000 0.61025814 10.00000000 0.1734226
## 5: AFATINIB BALL-1 1.0000000 0.04231953 3.16255534 0.8904389
## 6: AFATINIB BB30-HNC 1.0566193 0.35698201 0.01839543 0.8695942
## aac_recomputed ic50_recomputed
## <num> <num>
## 1: 21.020562 2.0011360
## 2: 21.016280 2.0019519
## 3: 43.183496 0.3985746
## 4: 8.086713 10.1235597
## 5: 16.729081 3.1652344
## 6: 75.201470 0.0185206## <PharmacoSet>
## Name: gCSI
## Date Created: Fri Apr 19 17:53:53 2024
## Number of samples: 795
## Molecular profiles:
## A MultiAssayExperiment object of 6 listed
## experiments with user-defined names and respective classes.
## Containing an ExperimentList class object of length 6:
## [1] genes: RangedSummarizedExperiment with 63187 rows and 675 columns
## [2] transcripts: RangedSummarizedExperiment with 252930 rows and 675 columns
## [3] genes_counts: RangedSummarizedExperiment with 63187 rows and 675 columns
## [4] transcripts_counts: RangedSummarizedExperiment with 252930 rows and 675 columns
## [5] genes_length: RangedSummarizedExperiment with 63187 rows and 675 columns
## [6] transcripts_length: RangedSummarizedExperiment with 252930 rows and 675 columns
## Treatment response:
## <TreatmentResponseExperiment>
## dim: 4365 569
## assays(2): sensitivity summary
## rownames(4365): 17-AAG:17AAG:6a:0.0015241580352681 17-AAG:17AAG:6a:0.00457247142398639 ... Vorinostat:VORINOSTAT:7i:3.33333528837956 Vorinostat:VORINOSTAT:7i:10
## rowData(4): treatmentid gCSI.treatmentid ExperimentNumber dose
## colnames(569): 22Rv1:22RV1 769-P:769P 8305C:8305C ... YMB-1-E:YMB1E ZR-75-1:ZR751 huH-1:HUH1
## colData(2): sampleid gCSI.sampleid
## metadata(0): none## <PharmacoSet>
## Name: gCSI
## Date Created: Wed Apr 5 21:23:39 2023
## Number of samples: 788
## Molecular profiles:
## Kallisto_0.46.1.rnaseq :
## Dim: 60662, 675
## Kallisto_0.46.1.rnaseq.counts :
## Dim: 60662, 675
## Kallisto_0.46.1.isoforms :
## Dim: 227912, 675
## Kallisto_0.46.1.isoforms.counts :
## Dim: 227912, 675
## CNV :
## Dim: 26291, 329
## mutation :
## Dim: 55, 329
## Treatment response:
## Drug pertubation:
## Please look at pertNumber(cSet) to determine number of experiments for each drug-sample combination.
## Drug sensitivity:
## Number of Experiments: 16688
## Please look at sensNumber(cSet) to determine number of experiments for each drug-sample combination.Old Sample Info
## --------------------------------------------------------------------------------
## Old Sample Info
## --------------------------------------------------------------------------------
## Num Samples in Old: 788
## [1] "Sample Info Columns"
## [1] "EMT" "DoublingTime"
## [3] "SeedingDensity" "isBlood"
## [5] "isBone" "isBone.Marrow"
## [7] "isBrain" "isBreast"
## [9] "isCervix" "isColon"
## [11] "isConnective.Tissue" "isEsophagus"
## [13] "isHead.and.Neck" "isKidney"
## [15] "isLiver" "isLung"
## [17] "isLymphoid" "isMuscle"
## [19] "isOvary" "isPancreas"
## [21] "isProstate" "isSkin"
## [23] "isSmall.Intestine" "isStomach"
## [25] "isUnclassified" "isUninary"
## [27] "isUterus" "DNADamageMutation"
## [29] "PI3K" "MAPK"
## [31] "tissueid" "sampleid"
## [33] "Cellosaurus.Disease.Type" "Cellosaurus.Accession.id"
## [35] "PharmacoDB.id" "unique.tissueid.fromstudies"
## [37] "CellLine.Type" "Metastatic"New Sample Info
## --------------------------------------------------------------------------------
## New Sample Info
## --------------------------------------------------------------------------------
## Num Samples in New: 795
## [1] "Sample Info Columns"
## [1] "gCSI.CellLineName" "gCSI.PrimaryTissue"
## [3] "gCSI.Norm_CellLineName" "EGA.ENA_ALIAS"
## [5] "EGA.TissueSupergroup" "EGA.MetastaticTissue"
## [7] "EGA.Disease" "EGA.Media"
## [9] "EGA.FreezeMedia" "EGA.Age"
## [11] "EGA.Sex" "EGA.Ethnicity"
## [13] "EGA.Protocol_REF" "EGA.AssayName"
## [15] "EGA.ScanName" "cellosaurus.cellLineName"
## [17] "cellosaurus.accession" "cellosaurus.category"
## [19] "cellosaurus.date" "cellosaurus.ageAtSampling"
## [21] "cellosaurus.sexOfCell" "cellosaurus.synonyms"
## [23] "cellosaurus.diseases" "gCSI.sampleid"
## [25] "sampleid"Old Treatment Info
## --------------------------------------------------------------------------------
## Old Treatment Info
## --------------------------------------------------------------------------------
## Num Samples in Old Treatment Info: 44
## [1] "Treatment Info Columns"
## [1] "treatmentid" "smiles" "inchikey" "cid" "FDA"New Treatment Info
## --------------------------------------------------------------------------------
## New Treatment Info
## --------------------------------------------------------------------------------
## Num Samples in New Treatment Info: 42
## [1] "Treatment Info Columns"
## [1] "unichem.ChEMBL" "pubchem.CID"
## [3] "gCSI.norm_treatmentid" "gCSI.treatmentid"
## [5] "pubchem.MolecularFormula" "pubchem.MolecularWeight"
## [7] "pubchem.InChIKey" "pubchem.Title"
## [9] "unichem.ChEBI" "unichem.clinicaltrials"
## [11] "unichem.DrugBank" "unichem.FDA_SRS"
## [13] "unichem.LINCS" "unichem.NIH_Clinical_Collection"
## [15] "unichem.PharmGKB" "unichem.rxnorm"
## [17] "chembl.parent_molecule_chembl_id" "chembl.target_chembl_id"
## [19] "chembl.record_id" "chembl.mechanism_of_action"
## [21] "chembl.mechanism_comment" "chembl.action_type"
## [23] "treatmentid"## --------------------------------------------------------------------------------
## Old Molecular Profiles with Annotation: microarray/rna
## --------------------------------------------------------------------------------
## No old molecular profiles with annotation
## --------------------------------------------------------------------------------
## New Molecular Profiles with Annotation: microarray/rna
## --------------------------------------------------------------------------------
## No new molecular profiles with annotationfor the OLD gCSI RNASeq data, the data is
transformed as follows: based on the orcestra
page for gCSI -
Gene TPM Values: After estimation by the tool detailed above, gene TPM values are transformed by log2(x + 0.001).
-
Gene Count Values: After estimation by the tool detailed above, gene count values are transformed by log2(x + 1).
## --------------------------------------------------------------------------------
## Old Molecular Profiles with Annotation: rnaseq
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: Kallisto_0.46.1.rnaseq
## [1] "Assay Names: exprs"
## [1] "Num Samples: 60662"
## [1] "Num Features: 675"
## [1] "No Description"
## SummarizedExperiment Name: Kallisto_0.46.1.rnaseq.counts
## [1] "Assay Names: exprs"
## [1] "Num Samples: 60662"
## [1] "Num Features: 675"
## [1] "No Description"
## --------------------------------------------------------------------------------
## New Molecular Profiles with Annotation: rnaseq
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: genes
## [1] "Assay Names: expr"
## [1] "Num Samples: 63187"
## [1] "Num Features: 675"
## [1] "No Description"
## SummarizedExperiment Name: transcripts
## [1] "Assay Names: expr"
## [1] "Num Samples: 252930"
## [1] "Num Features: 675"
## [1] "No Description"
## SummarizedExperiment Name: genes_counts
## [1] "Assay Names: expr"
## [1] "Num Samples: 63187"
## [1] "Num Features: 675"
## [1] "No Description"
## SummarizedExperiment Name: transcripts_counts
## [1] "Assay Names: expr"
## [1] "Num Samples: 252930"
## [1] "Num Features: 675"
## [1] "No Description"
## SummarizedExperiment Name: genes_length
## [1] "Assay Names: expr"
## [1] "Num Samples: 63187"
## [1] "Num Features: 675"
## [1] "No Description"
## SummarizedExperiment Name: transcripts_length
## [1] "Assay Names: expr"
## [1] "Num Samples: 252930"
## [1] "Num Features: 675"
## [1] "No Description"## --------------------------------------------------------------------------------
## Old Molecular Profiles with Annotation: cnv
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: cnv
## [1] "Assay Names: exprs"
## [1] "Num Samples: 26291"
## [1] "Num Features: 329"
## [1] "No Description"
## --------------------------------------------------------------------------------
## New Molecular Profiles with Annotation: cnv
## --------------------------------------------------------------------------------
## No new molecular profiles with annotation## --------------------------------------------------------------------------------
## Old Molecular Profiles with Annotation: mutation/mut
## --------------------------------------------------------------------------------
## SummarizedExperiment Name: mutation
## [1] "Assay Names: exprs"
## [1] "Num Samples: 55"
## [1] "Num Features: 329"
## [1] "No Description"
## --------------------------------------------------------------------------------
## New Molecular Profiles with Annotation: mutation/mut
## --------------------------------------------------------------------------------
## No new molecular profiles with annotation## --------------------------------------------------------------------------------
## Old Treatment Response
## --------------------------------------------------------------------------------
## Old Treatment Response is a list of DataFrames
## [1] "Number of treatments: 44"
## [1] "Number of samples: 569"
## [1] "Total number of experiments: 16688"
## [1] "Profiles DataFrame: "
## aac_recomputed ic50_recomputed HS E_inf EC50
## 22Rv1_17-AAG_6a 0.23181647 1.081040 1.386410 28.179810 0.5944260
## 22Rv1_5-FU_8g 0.25059450 NA 1.723254 56.201823 1.3085159
## 22Rv1_AZ-628_8g 0.15030690 3.039147 2.267915 47.522132 0.8079433
## 22Rv1_Cisplatin_6a 0.01067784 NA 4.000000 88.631298 44.2150896
## 22Rv1_Cisplatin_8g 0.28197159 3.941812 1.519334 6.011569 3.6230991
## 22Rv1_GDC-0941_6a 0.24497744 1.097340 1.560266 47.327876 0.1678894
## GR_AOC_published meanviability_published GRmax_published
## 22Rv1_17-AAG_6a 0.29333333 0.7545167 0.130
## 22Rv1_5-FU_8g 0.27966667 0.7448983 0.495
## 22Rv1_AZ-628_8g 0.16633333 0.8559627 0.342
## 22Rv1_Cisplatin_6a -0.01744444 1.0191022 0.890
## 22Rv1_Cisplatin_8g 0.42833333 0.6913101 -0.606
## 22Rv1_GDC-0941_6a 0.23375000 0.7918895 0.361
## Emax_published GRinf_published GEC50_published
## 22Rv1_17-AAG_6a 0.30894488 0.08861534 7.315019e-07
## 22Rv1_5-FU_8g 0.54816000 0.51229424 1.419045e-06
## 22Rv1_AZ-628_8g 0.43983110 0.38020802 9.074455e-07
## 22Rv1_Cisplatin_6a 0.89060009 1.01744444 0.000000e+00
## 22Rv1_Cisplatin_8g 0.03543224 -0.92702240 1.069242e-05
## 22Rv1_GDC-0941_6a 0.45316145 0.38887158 1.896307e-07
## GR50_published
## 22Rv1_17-AAG_6a 8.402577e-07
## 22Rv1_5-FU_8g Inf
## 22Rv1_AZ-628_8g 1.871457e-06
## 22Rv1_Cisplatin_6a Inf
## 22Rv1_Cisplatin_8g 3.583645e-06
## 22Rv1_GDC-0941_6a 5.073825e-07
## --------------------------------------------------------------------------------
## New Treatment Response
## --------------------------------------------------------------------------------
## New Treatment Response is a TreatmentResponseExperiment
## [1] "Number of treatments: 42"
## [1] "Number of samples: 569"
## [1] "Total number of experiments: 141756"
## [1] "Profiles/Summary Assay: "
## Key: <treatmentid, gCSI.treatmentid, ExperimentNumber, dose, sampleid, gCSI.sampleid>
## treatmentid gCSI.treatmentid ExperimentNumber dose sampleid
## <char> <char> <char> <num> <char>
## 1: 17-AAG 17AAG 6a 0.001524158 22Rv1
## 2: 17-AAG 17AAG 6a 0.001524158 A-375
## 3: 17-AAG 17AAG 6a 0.001524158 A-427
## 4: 17-AAG 17AAG 6a 0.001524158 A2780
## 5: 17-AAG 17AAG 6a 0.001524158 A549
## 6: 17-AAG 17AAG 6a 0.001524158 AGS
## gCSI.sampleid GR activities.mean activities.std
## <char> <num> <num> <num>
## 1: 22RV1 1.003 0.3104185 4.4933546
## 2: A375 1.015 2.1585380 0.2984795
## 3: A427 1.036 4.3378962 7.0766344
## 4: A2780 1.062 11.6888332 11.8974871
## 5: A549 1.006 0.6713567 5.0588595
## 6: AGS 1.025 3.7235839 2.3278981