biomart_stats: Get Gene Length and GC: biomart

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

Get Gene Length and GC: biomart

Description

Get gene length and 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

biomart_stats(gene, column_id, df, start, end)

Arguments

gene	a gene name corresponding to a value in 'df[,column_id]'
column_id	the column name containg gene feature IDs
df	the dataframe of exon/transcript annotations
start	column name of feature start coordinate
end	column name of feature end coordinate

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