geneEnrichment: geneEnrichment

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 length-corrected genes A 'gene_lengths' file must be provided with the following fields (cols 1..6 required) gene length chrom start end tss scaling_factor 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

geneEnrichment(..., snv_data = NULL,
  gene_lengths_in = "data/gene_lengths.txt", n = 10,
  genome_length = 118274340, write = FALSE)

Arguments

n	The number of times we need to have seen a gene in our snv_data to view its enrichment score [Default 3]
genome_length	The total legnth of the genome [Default 137547960 (chroms 2, 3, 4, X & Y for Drosophila melanogastor Dmel6.12)]
gene_lengths	File containing all genes and their lengths (as generated by 'script/genomefeatures.pl') [Default 'data/gene_lengths.txt']

Details

Function to calculate fold change enrichment in a set of snv calls correcting for gene length

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.