makegenelist: Generate a GRanges object of UCSC known genes in specific...

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

Generate a GRanges object of UCSC known genes in specific genome

Description

Generate a GRanges object of UCSC known genes in specific genome.

Usage

makegenelist(
  genomename = "mm10",
  save = TRUE,
  calgenegccont = TRUE,
  calgeneexonfreq = TRUE
)

Arguments

genomename	The name of the genome, can be "mm10" for mouse or "hg38" for human.
save	Whether save the result GRanges as a file in work directory. Default is TRUE.
calgenegccont	Whether need to calculate the GC content for each gene and include it into the result GRanges object. Default is TRUE.
calgeneexonfreq	Whether calculate the exon frequency for each gene and include it into the result GRanges object. Default is TRUE.

Value

A GRanges object of UCSC known genes, with several gene information provided, including seqnames, ranges, strands, gene symbols, distance to the nearest upstream gene, distance to the nearest downstream gene, etc. Genes overlapping with each other will not be included.

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