read_expression_data: Reading gene expression data from file

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

Reading gene expression data from file

Description

Reads gene expression matrix data file which is either tab/comma/white-space value separated text file. After reading in the input file, any gene rows that contain NAs are removed and the data set is screened for duplicates. Duplicate genes are reduced to single gene row entries, with each value corresponding to the mean expression value for each sample for the duplicated gene entry. If duplicate samples are detected then the only the first sample of the duplicates are retained. Finally, the data frame is converted to a numerical matrix, where row names represent gene symbols and columns represent sample names or IDs.

Usage

read_expression_data(file)

Arguments

file	Path for gene expression matrix file, which is either tab / comma / white-space value separated. The first column must contain gene symbols and the subsequent column names should be the sample name or ID.

Value

A numerical matrix containing gene symbols/IDs as row names and sample IDs as column names.

Author(s)

Taniya Pal [e-mail]

Examples

## Not run: read_expr_data("/Users/taniyapal/Documents/Group Project/TCGA_unannotated.txt")

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