get_Pfam_domain: Function to annotate fusion calls with domain terms

Description Usage Arguments Value Examples

View source: R/get_Pfam_domain.R

Description

Function to annotate fusion calls with domain terms

Usage

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get_Pfam_domain(standardFusioncalls, bioMartDataPfam, keepPartialAnno = FALSE)

Arguments

standardFusioncalls

A dataframe from star fusion or arriba standardized to run through the filtering steps

bioMartDataPfam

A dataframe with gene and domain coordinate information with chromosome_name,gene_start,gene_end,domain_chr,domain_start,domain_end,hgnc_symbol

keepPartialAnno

TRUE or FALSE to keep partial status; defaults to FALSE

Value

Standardized fusion calls as list Gene1A and Gene1B annotated with domain terms and chromosome location; retained and not retained,optionally partially retained

Examples

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out_annofuse <- system.file("extdata", "PutativeDriverAnnoFuse.tsv", package = "annoFuseData")
sfc <- read.delim(out_annofuse)
bioMartDataPfam <- readRDS(system.file("extdata", "pfamDataBioMart.RDS", package = "annoFuseData"))
domain_list_df <- get_Pfam_domain(standardFusioncalls = sfc, bioMartDataPfam = bioMartDataPfam)

d3b-center/annoFuse documentation built on March 11, 2021, 9:05 p.m.