featureEnrichment: featureEnrichment

In nriddiford/mutationProfiles: Collection of functions to explore SNV data (e.g. Mutect2/Freebayes) parsed by get_tris.pl

Description

Calculate the enrichment of snv hits in genomic features A 'features' file must be provided with the follwing format: feature length percentage This can be generated using the script 'script/genomic_features.pl' and a genome .gtf file The defualt genome length is set to the mappable regions of the Drosophila melanogastor Dmel6.12 genome (GEM mappability score > .5) (118274340). The full, assembled genome legnth for chroms 2/3/4/X/Y is 137547960

Usage

featureEnrichment(..., snv_data = NULL,
  features = "data/genomic_features.txt", genome_length = 118274340,
  write = FALSE)

Arguments

features	File containing total genomic lengths of features [Default 'data/genomic_features.txt']
genome_length	The total legnth of the genome [Default 118274340 (mappable regions on chroms 2, 3, 4, X & Y for Drosophila melanogastor Dmel6.12)]

Details

Function to calculate enrichment of snv hits in genomic features

Value

A snv_data frame with FC scores for all genes seen at least n times in snv snv_data

nriddiford/mutationProfiles documentation built on Nov. 7, 2021, 12:14 a.m.