pfamDomains: pfam domain annotation and summarization.

In thesushantpatil/maftools: Summarize, Analyze and Visualize MAF Files

Description

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

Usage

pfamDomains(
  maf = NULL,
  AACol = NULL,
  summarizeBy = "AAPos",
  top = 5,
  domainsToLabel = NULL,
  baseName = NULL,
  varClass = "nonSyn",
  width = 5,
  height = 5,
  labelSize = 1
)

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.
domainsToLabel	Default NULL. Exclusive with top argument.
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.
width	width of the file to be saved.
height	height of the file to be saved.
labelSize	font size for labels. Default 1.

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

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
pfamDomains(maf = laml, AACol = 'Protein_Change')

thesushantpatil/maftools documentation built on May 18, 2020, 9:54 p.m.