getgc: Calculate GC content 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 GC content for specific gene regions

Description

Calculate GC content for specific genes regions.

Usage

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

Arguments

targetfile	The directory of the file indicating the gene regions whose GC contents 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 GC contents need to be calculated. The default value is NULL. If it is set, for the regions indicated by the parameter targetfile or genomename, they will be analyzed only when they also belong to the genes indicated by this parameter genenames.

Value

A data.frame with a column named GC indicating the GC contents of the gene regions.

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