maftools (version 0.99.30)

MAF-class: Class MAF

Description

S4 class for storing summarized MAF.

Slots

data

data.table of original MAF file.

variants.per.sample

table containing variants per sample

variant.type.summary

table containing variant types per sample

variant.classification.summary

table containing variant classification per sample

gene.summary

table containing variant classification per gene

oncoMatrix

character matrix of dimension n*m where n is number of genes and m is number of variants

numericMatrix

numeric matrix of dimension n*m where n is number of genes and m is number of variants

summary

table with basic MAF summary stats

classCode

mapping between numeric values in numericMatrix and Variant Classification

maf.silent

subset of main MAF containing only silent variants

See Also

getGeneSummary getSampleSummary getFields