get_ctrl_tx: Get Control Transcript list from Case gene list

In TaliaferroLab/rnareachr: Extract Enriched Biological Features From RNA-seq Data

Description

This will return transcripts representing all other genes not in gene_list This requires creating a length_df see make_longest or make_median. Generating a control transcript list with this function isn't recommended as not all genes will be exprsesed in a given system.It is best to use expression data from your system to create a list of expressed control transcripts.

Usage

get_ctrl_tx(length_df, gene_list, seq_type)

Arguments

length_df	A dataframe relating genes and transcritps by their length. Should be the output from make_longest or make_median.
gene_list	A character list of ensembl gene IDs.
seq_type	One of "whole", "CDS", "5UTR" or "3UTR".

Value

a character list of ensembl transcript IDs.

Examples

mm_case_gene <- c("ENSMUSG00000097392", "ENSMUSG00000025607", "ENSMUSG00000030671", "ENSMUSG00000034764", "ENSMUSG00000116215", "ENSMUSG00000039556", "ENSMUSG00000066510", "ENSMUSG00000018160", "ENSMUSG00000114306", "ENSMUSG00000028277", "ENSMUSG00000037216", "ENSMUSG00000032299") #12genes
get_ctrl_tx(longest_mm, mm_case_gene, "UTR3")

TaliaferroLab/rnareachr documentation built on Aug. 15, 2021, 5:37 p.m.