gimme_expr_mat: Extract the gene expression counts from an vast-tools...

In Ni-Ar/niar: Nice Interactive Analysis with R

Extract the gene expression counts from an vast-tools expression table and return them as a matrix

Description

The matrix contains the samples as row names and the gene ID as column name. The gene ID used are the one present in the first column of the table (usually ENSEMBL gene ID).

Usage

gimme_expr_mat(vst_expression_tbl, min_mean_count = 5, verbose = FALSE)

Arguments

vst_expression_tbl	Path to a vast-tools expression table (either cRPKM or TPM).
min_mean_count	Filter out low expressed genes in the table read from inclusion_tbl. Defines the minimum row mean expression value across all samples that a gene must have to be selected.
verbose	Print out extra info.

Value

A matrix

Examples

gimme_expr_mat(vst_expression_tbl = /path/to/expr/table/file.tab)

Ni-Ar/niar documentation built on Feb. 3, 2025, 9:25 a.m.