pfam domain annotation and summarization.
Summarizes amino acid positions and annotates them with pfam domain information.
pfamDomains( maf = NULL, AACol = NULL, summarizeBy = "AAPos", top = 5, domainsToLabel = NULL, baseName = NULL, varClass = "nonSyn", width = 5, height = 5, labelSize = 1 )
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. |
returns a list two tables summarized by amino acid positions and domains respectively. Also plots top 5 most mutated domains as scatter plot.
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
pfamDomains(maf = laml, AACol = 'Protein_Change')Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.