maftools (version 0.99.30)

pfamDomains: pfam domain annotation and summarization.

Description

Summarizes amino acid positions and annotates them with pfam domain information.

Usage

pfamDomains(maf = NULL, AACol = NULL, summarizeBy = "AAPos", top = 5,
  baseName = NULL, varClass = "nonSyn")

Arguments

maf

an MAF object generated by read.maf

AACol

manually specify column name for amino acid changes. Default looks for field 'AAChange'

summarizeBy

Summarize domains by amino acid position or conversions. Can be "AAPos" or "AAChange"

top

How many top mutated domains to label in the scatter plot. Defaults to 5.

baseName

If given writes the results to output file. Default NULL.

varClass

which variants to consider for summarization. Can be nonSyn, Syn or all. Default nonSyn.

Value

returns a list two tables summarized by amino acid positions and domains respectively. Also plots top 5 most mutated domains as scatter plot.

Examples

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE)
pfamDomains(maf = laml, AACol = 'Protein_Change')
# }