Gather Mutations for TCGA Datasets

Description

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

Usage

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

Arguments

Issues

If you have any problems, issues or think that something is missing or is not clear please post an issue on https://github.com/RTCGA/RTCGA/issues.

Note

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

Author(s)

Marcin Kosinski, m.p.kosinski@gmail.com

See Also

RTCGA website http://rtcga.github.io/RTCGA/Visualizations.html.

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

Examples

library(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(!is.na(Variant_Classification), "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"),
			 break.time.by = 400, xlim = c(0,2000))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RTCGA)
Welcome to the RTCGA (version: 1.2.2).
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RTCGA/mutationsTCGA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mutationsTCGA
> ### Title: Gather Mutations for TCGA Datasets
> ### Aliases: mutationsTCGA
> 
> ### ** Examples
> 
> 
> library(RTCGA)
> library(RTCGA.mutations)
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 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(!is.na(Variant_Classification), "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"),
+ 			 break.time.by = 400, xlim = c(0,2000))
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>