metaITH_analysis: Runs a comprehensive intratumor heterogeneity analysis

In Elise-Merritt/metaITH: A Tool for Analyzing Intratumor Heterogeneity at Multiple Levels

Description

Analyzes several sample files by running a dendrogram analysis (using DNA, RNA, and immune expression data), signature analysis (using RNA expression data), and multi-region diversity and divergence analysis (using DNA, RNA, and immune expression data)

Usage

metaITH_analysis(dna_dendro_list, rna_dendro_list, immune_dendro_list, multi_region_sample_names, rna_expression_matrix)

Arguments

dna_dendro_list	A text file containing a list of sample files, one file name per line. Each file contains a matrix with variant allele frequency of all the variations in each tumor region and normal.
rna_dendro_list	A text file containing a list of sample files, one file name per line. Each file contains a matrix with expression values (preferably log2(TPM+1)) of all the genes in each tumor region and normal.
immune_dendro_list	A text file containing a list of sample files, one file name per line. Each file contains a matrix with proportion of immune cells (inferred by CIBERSORT) of all immune cell types in each tumor region and normal.
multi_region_sample_names	A text file containing list of sample names for multi-region diversity and divergence analysis, one file name per line
rna_expression_matrix	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"

Elise-Merritt/metaITH documentation built on Sept. 13, 2019, 12:57 a.m.