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Get available genetic data profiles for a specific cancer study

Usage

geneticProfiles(cancerStudy)

Arguments

cancerStudy

character(1). Cancer study identifier (e.g. "ccle_broad_2019"). Refer to cancerStudies() for details.

Value

DataFrame.

Note

Updated 2022-06-06.

Examples

x <- geneticProfiles(cancerStudy = "ccle_broad_2019")
print(x)
#> DataFrame with 11 rows and 6 columns
#>                                                              geneticProfileId
#>                                                                   <character>
#> ccle_broad_2019_CCLE_drug_treatment_AUC                ccle_broad_2019_CCLE..
#> ccle_broad_2019_CCLE_drug_treatment_IC50               ccle_broad_2019_CCLE..
#> ccle_broad_2019_CCLE_drug_treatment_zscore             ccle_broad_2019_CCLE..
#> ccle_broad_2019_cna                                       ccle_broad_2019_cna
#> ccle_broad_2019_fusion                                 ccle_broad_2019_fusion
#> ccle_broad_2019_mutations                              ccle_broad_2019_muta..
#> ccle_broad_2019_protein_quantification                 ccle_broad_2019_prot..
#> ccle_broad_2019_protein_quantification_zscores         ccle_broad_2019_prot..
#> ccle_broad_2019_rna_seq_mrna                           ccle_broad_2019_rna_..
#> ccle_broad_2019_rna_seq_mrna_median_Zscores            ccle_broad_2019_rna_..
#> ccle_broad_2019_rna_seq_mrna_median_all_sample_Zscores ccle_broad_2019_rna_..
#>                                                            geneticProfileName
#>                                                                   <character>
#> ccle_broad_2019_CCLE_drug_treatment_AUC                Treatment response: ..
#> ccle_broad_2019_CCLE_drug_treatment_IC50               Treatment response: ..
#> ccle_broad_2019_CCLE_drug_treatment_zscore             Treatment response: ..
#> ccle_broad_2019_cna                                    Copy Number Alterati..
#> ccle_broad_2019_fusion                                                Fusions
#> ccle_broad_2019_mutations                                           Mutations
#> ccle_broad_2019_protein_quantification                 Protein abundance ra..
#> ccle_broad_2019_protein_quantification_zscores         Z-scores of protein ..
#> ccle_broad_2019_rna_seq_mrna                           mRNA expression (RNA..
#> ccle_broad_2019_rna_seq_mrna_median_Zscores            mRNA expression z-sc..
#> ccle_broad_2019_rna_seq_mrna_median_all_sample_Zscores mRNA expression z-sc..
#>                                                        geneticProfileDescription
#>                                                                      <character>
#> ccle_broad_2019_CCLE_drug_treatment_AUC                   Area under the sigmo..
#> ccle_broad_2019_CCLE_drug_treatment_IC50                  IC50 values (in micr..
#> ccle_broad_2019_CCLE_drug_treatment_zscore                Z-scores of the ln-t..
#> ccle_broad_2019_cna                                       Copy number alterati..
#> ccle_broad_2019_fusion                                              Fusion data.
#> ccle_broad_2019_mutations                                 Whole-exome sequenci..
#> ccle_broad_2019_protein_quantification                    Protein abundance ra..
#> ccle_broad_2019_protein_quantification_zscores            Z-scores of protein ..
#> ccle_broad_2019_rna_seq_mrna                              Expression levels fo..
#> ccle_broad_2019_rna_seq_mrna_median_Zscores               mRNA z-Scores (RNA S..
#> ccle_broad_2019_rna_seq_mrna_median_all_sample_Zscores    Log-transformed mRNA..
#>                                                        cancerStudyId
#>                                                            <integer>
#> ccle_broad_2019_CCLE_drug_treatment_AUC                          415
#> ccle_broad_2019_CCLE_drug_treatment_IC50                         415
#> ccle_broad_2019_CCLE_drug_treatment_zscore                       415
#> ccle_broad_2019_cna                                              415
#> ccle_broad_2019_fusion                                           415
#> ccle_broad_2019_mutations                                        415
#> ccle_broad_2019_protein_quantification                           415
#> ccle_broad_2019_protein_quantification_zscores                   415
#> ccle_broad_2019_rna_seq_mrna                                     415
#> ccle_broad_2019_rna_seq_mrna_median_Zscores                      415
#> ccle_broad_2019_rna_seq_mrna_median_all_sample_Zscores           415
#>                                                         geneticAlterationType
#>                                                                   <character>
#> ccle_broad_2019_CCLE_drug_treatment_AUC                         GENERIC_ASSAY
#> ccle_broad_2019_CCLE_drug_treatment_IC50                        GENERIC_ASSAY
#> ccle_broad_2019_CCLE_drug_treatment_zscore                      GENERIC_ASSAY
#> ccle_broad_2019_cna                                    COPY_NUMBER_ALTERATION
#> ccle_broad_2019_fusion                                     STRUCTURAL_VARIANT
#> ccle_broad_2019_mutations                                   MUTATION_EXTENDED
#> ccle_broad_2019_protein_quantification                          PROTEIN_LEVEL
#> ccle_broad_2019_protein_quantification_zscores                  PROTEIN_LEVEL
#> ccle_broad_2019_rna_seq_mrna                                  MRNA_EXPRESSION
#> ccle_broad_2019_rna_seq_mrna_median_Zscores                   MRNA_EXPRESSION
#> ccle_broad_2019_rna_seq_mrna_median_all_sample_Zscores        MRNA_EXPRESSION
#>                                                        showProfileInAnalysisTab
#>                                                                     <character>
#> ccle_broad_2019_CCLE_drug_treatment_AUC                                    true
#> ccle_broad_2019_CCLE_drug_treatment_IC50                                   true
#> ccle_broad_2019_CCLE_drug_treatment_zscore                                 true
#> ccle_broad_2019_cna                                                        true
#> ccle_broad_2019_fusion                                                     true
#> ccle_broad_2019_mutations                                                  true
#> ccle_broad_2019_protein_quantification                                    false
#> ccle_broad_2019_protein_quantification_zscores                             true
#> ccle_broad_2019_rna_seq_mrna                                              false
#> ccle_broad_2019_rna_seq_mrna_median_Zscores                                true
#> ccle_broad_2019_rna_seq_mrna_median_all_sample_Zscores                     true