DEPTH: Evaluation of the tumor heterogeneity level.

In WangX-Lab/DEPTH: Tumor heterogeneity level evaluation

Evaluation of the tumor heterogeneity level.

Description

DEPTH DEPTH evaluates the tumor heterogeneity level of each tumor sample based on gene expression profiles Heterogeneity score vignette.

Usage

DEPTH(exp, match)

Arguments

exp

gene expression profiles in both tumor and normal samples (microarray or RNA-Seq data, log2 transformed is recommended). DEPTH function support 2 kind of datasets: 1) if the "exp" dataset has normal samples and tumor samples, we can caculate the heterogeneity score with both normal samples and tumor samples. 2) else if the "exp" dataset only has tumor samples, we can caculate the heterogeneity score by with tumor samples.

match

samples in "exp" denoted by "Tumor" or "Normal".

Details

DEPTH evaluates the tumor heterogeneity level of each tumor sample based on gene expression profiles.

Value

A matrix with 2 columns:

Sample	Tumor samples to be predicted.
heterogeneity score	The heterogeneity score of each sample.

Author(s)

Xiaosheng Wang <[e-mail]>

WangX-Lab/DEPTH documentation built on July 4, 2022, 7:55 p.m.