signature_analysis: Runs a signature analysis on an RNA expression matrix

In sjdlabgroup/metaITH: A Tool for Analyzing Intratumor Heterogeneity at Multiple Levels

Description

Takes in RNA expression matrix containing the expression level of all genes in all tumor samples and normals. Creates a z-score matrix and uses this matrix to find the hypoxia, proliferation, apoptosis, drug-resistance, emt, and anti-PD1 favor scores for each tumor sample or region. Outputs a table and heatmap of these scores.

Usage

signature_analysis(rna_expression_matrix_file, type)

Arguments

rna_expression_matrix_file	File containing expression level of all genes in all tumor samples. Header of first column should be "Gene" and each normal file should end in ".nr"
type	String specifying type of analysis. Options are "all", "hypoxia", "proliferation", "apoptosis", "drug-resistance", "emt", "anti-PD1". Default parameter is "all".

sjdlabgroup/metaITH documentation built on Nov. 5, 2019, 8:58 a.m.