pfamDomains {maftools} | R Documentation

## 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,
      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')

[Package maftools version 2.10.05 Index]