getexon: Calculate exon coverages for specific gene regions

In yuabrahamliu/proRate: proRate is an R package to infer gene transcription rates with a novel least sum of squares method.

Calculate exon coverages for specific gene regions

Description

Calculate exon coverages for specific genes regions.

Usage

getexon(targetfile = NULL, genomename = "mm10", genenames = NULL)

Arguments

targetfile	The directory of the file indicating the gene regions whose exon coverages need to be calculated, not necessary to be exactly the gene body region between TSS and TTS sites. Columns named as chr, start, end, strand, and gene_id are required. If it is NULL, all the gene body regions of UCSC known genes in the genome specified by the parameter genomename will be analyzed.
genomename	Specify the genome of the genes to be analyzed, when the parameter targetfile is NULL.
genenames	The symbols of genes whose exon coverages need to be calculated. The regions indicated by the parameter targetfile or genomename will be analyzed only if they belong to the genes indicated by this parameter genenames.

Value

A data.frame with a column named exon indicating the exon coverages of the gene regions.

yuabrahamliu/proRate documentation built on Nov. 3, 2024, 10:14 a.m.