read_signature: Reads up-regulated and down-regulated gene signatures from...

In a-thind/PathAnalyser: ER & HER2 Pathway Activity Analysis For Breast Cancer Transcriptomic Datasets

Reads up-regulated and down-regulated gene signatures from gene set files

Description

Reads up and down regulated signature files provided either in gene set file format (.grp) or gene matrix transposed format (.gmt) creating a data frame which the first column named "gene" containing the gene symbols and the second column called "expression" containing the corresponding expression value for a gene in the gene signature, where 1 signifies up-regulation and -1 represents down-regulation of the gene in the gene signature.

Usage

read_signature(up_sig_file, down_sig_file)

Arguments

up_sig_file	Up-regulated gene-set format file
down_sig_file	Down-regulated gene-set format file

Value

A data frame containing both up regulated and down regulated signature files and signifying their up or down expression with +1 and -1 respectively.

Author(s)

Taniya Pal [e-mail]

Examples

## Not run: read_sign_data("ESR1_UP.v1._UP.csv","ESR1_DN.v1_DN.csv" )

a-thind/PathAnalyser documentation built on May 6, 2022, 9:50 a.m.