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Takes tab delimited MAF (can be plain text or gz compressed) file as an input and summarizes it in various ways. Also creates oncomatrix - helpful for visualization.
read.maf(maf, removeSilent = TRUE, useAll = FALSE)
tab delimited MAF file. File can also be gz compressed.
logical. Whether to discard silent (with no functional impact) mutations ("Silent","Intron","RNA","3'UTR"). Default is TRUE.
logical. Whether to use all variants irrespective of values in Mutation_Status. Defaults to False. Only uses with values Somatic.
An object of class MAF.
plotmafSummary write.mafSummary
plotmafSummary
write.mafSummary
# NOT RUN { laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools") laml <- read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE) # }
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