gtf_stats: Get Gene Length and GC: GTF/Fasta

In Sage-Bionetworks/sageseqr: Identify differentially expressed genes counts data

Get Gene Length and GC: GTF/Fasta

Description

Get gene GC content of 'gene' from data frame ('df') containing gene IDs in a column labeled the value of 'column_id'. 'df' must have a column labeled sequence where the sequence info for exons/or transcripts are and feature start and stop coordinates in columns labled the value of 'start' and 'stop'. This will return a vector of 'gene', length, and GC content as a percentage.

Usage

gtf_stats(i, data, genome)

Arguments

i	A character of a gene id.
data	a dataframe of exons transcrtipts or genes, imported from a GTF file. one line per-feature, data$V1 corresponds to the featur chormosome, data$V4 to start coordinate, data$V5 to stop coordinate, and data$V7 to the sequence strand.
genome	a list of DNAStringSet objects named by their contig (chromosome) name.

Sage-Bionetworks/sageseqr documentation built on June 13, 2024, 2:11 p.m.