tcgaCompare {maftools} | R Documentation |
Compares mutation load in input MAF against all of 33 TCGA cohorts derived from MC3 project.
tcgaCompare(maf, capture_size = NULL, tcga_capture_size = 50, cohortName = NULL, tcga_cohorts = NULL, primarySite = FALSE, col = c("gray70", "black"), bg_col = c("#EDF8B1", "#2C7FB8"), medianCol = "red")
maf |
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capture_size |
capture size for input MAF in MBs. Default NULL. If provided plot will be scaled to mutations per mb. TCGA capture size is assumed to be 50mb. |
tcga_capture_size |
capture size for TCGA cohort in MBs. Default 50 |
cohortName |
name for the input MAF cohort. Default "Input" |
tcga_cohorts |
restrict tcga data to these cohorts. |
primarySite |
If TRUE uses primary site of cancer as labels instead of TCGA project IDs. Default FALSE. |
col |
color vector for length 2 TCGA cohorts and input MAF cohort. Default gray70 and black. |
bg_col |
background color. Default'#EDF8B1', '#2C7FB8' |
medianCol |
color for median line. Default red. |
data.table with median mutations per cohort
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools") laml <- read.maf(maf = laml.maf) tcgaCompare(maf = laml, cohortName = "AML")