Function gathers mutations over multiple TCGA datasets and extracts mutations and further informations about them for desired genes. See mutations.

mutationsTCGA(..., extract.cols = c("Hugo_Symbol", "Variant_Classification",
  "bcr_patient_barcode"), extract.names = TRUE, unique = TRUE)


A data.frame or data.frames from TCGA study containing mutations information (RTCGA.mutations).
A character specifing the names of columns to be extracted with bcr_patient_barcode. If NULL all columns are returned.
Logical, whether to extract names of passed data.frames in ....
Should the outputed data be unique. By default it's TRUE.


Input data.frames should contain column bcr_patient_barcode if extract.cols is specified.


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See also

RTCGA website

Other RTCGA: RTCGA-package, boxplotTCGA, checkTCGA, convertTCGA, createTCGA, datasetsTCGA, downloadTCGA, expressionsTCGA, heatmapTCGA, infoTCGA, installTCGA, kmTCGA, pcaTCGA, readTCGA, survivalTCGA, theme_RTCGA


library(RTCGA.mutations) library(dplyr) mutationsTCGA(BRCA.mutations, OV.mutations) %>% filter(Hugo_Symbol == 'TP53') %>% filter(substr(bcr_patient_barcode, 14, 15) == "01") %>% # cancer tissue mutate(bcr_patient_barcode = substr(bcr_patient_barcode, 1, 12)) -> BRCA_OV.mutations library(RTCGA.clinical) survivalTCGA(BRCA.clinical, OV.clinical, extract.cols = "admin.disease_code") %>% rename(disease = admin.disease_code)-> BRCA_OV.clinical BRCA_OV.clinical %>% left_join(BRCA_OV.mutations, by = "bcr_patient_barcode") %>% mutate(TP53 = ifelse(!, "Mut", "WILDorNOINFO")) -> BRCA_OV.clinical_mutations BRCA_OV.clinical_mutations %>% select(times, patient.vital_status, disease, TP53) -> BRCA_OV.2plot kmTCGA(BRCA_OV.2plot, explanatory.names = c("TP53", "disease"), = 400, xlim = c(0,2000))