gene2Tx: Get transcript list from gene list

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

Description

gene2Tx takes a gene list and returns a list of transcripts with the longest or median length feature of interest.

Usage

gene2Tx(length_df, gene_list, seq_type)

Arguments

length_df	A data frame. Created by make_longest_df or make_median_df.
gene_list	A character list. Must contain Ensembl gene IDs and be compatible with the gff (the same species).
seq_type	One of "whole", "CDS", "5pUTR", or "3pUTR".

Value

gene2Tx returns a character list of Ensembl transcript IDs associated with the length and sequence type of interest.

See Also

filter_Tx, make_longest_df, make_median_df

Examples

hs_filtered_TxDb <- filter_Tx("mydata/Gencodedat/gencode.v33.annotation.gff3.gz")
longest_hs <- make_longest_df(hs_filtered_TxDb)
hs_gene <- c("ENSG00000000419.12", "ENSG00000001167.14", "ENSG00000000938.13")
hs_tx <- gene2Tx(longest_hs, hs_gene, "UTR3")

TaliaferroLab/FeatureReachR documentation built on Aug. 15, 2021, 2:21 p.m.