Get available genetic data profiles for a specific cancer study
Source:R/geneticProfiles.R
geneticProfiles.Rd
Get available genetic data profiles for a specific cancer study
Arguments
- cancerStudy
character(1)
. Cancer study identifier (e.g. "ccle_broad_2019"). Refer tocancerStudies()
for details.
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