mafSurvGroup {maftools} | R Documentation |
Similar to mafSurvival
but for a geneset
mafSurvGroup( maf, geneSet = NULL, minMut = NA, clinicalData = NULL, time = "Time", Status = "Status" )
maf |
|
geneSet |
gene names for which survival analysis needs to be performed. |
minMut |
minimum number of mutated genes in the 'geneSet' to consider a sample as a mutant. Default, 'NA', samples with all the genes mutated are treated as mutant group. |
clinicalData |
|
time |
column name containing time in |
Status |
column name containing status of patients in |
Survival plot
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools") laml.clin <- system.file("extdata", "tcga_laml_annot.tsv", package = "maftools") laml <- read.maf(maf = laml.maf, clinicalData = laml.clin) mafSurvGroup(maf = laml, geneSet = c('DNMT3A', 'FLT3'), time = 'days_to_last_followup', Status = 'Overall_Survival_Status')