DEPTH

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

Cite the code:

Description

This vignette shows an example of how to use the DEPTH algorithm to calculate tumor heterogeneity level in R.

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

Details

Input Two files need to be input into the DEPTH function:

1. exp: gene expression profiles in both tumor and normal samples (microarray or RNA-Seq data, normalized);

                              Table 1. RNA expression of input data
   

Identification	TCGA-A6-2671-11A-01R-A32Z-07	TCGA-A6-2675-11A-01R-1723-07	TCGA-A6-2675-01A-02R-1723-07
SKAP1	6.22	4.36	6.00
TPSB2	9.39	9.45	9.21
PLXNB3	6.09	8.45	4.95
VAT1L	7.45	7.76	6.13
VIP	9.43	10.99	7.71
WNT5B	7.52	7.80	6.29
ZAP70	6.43	5.13	5.94
TNFRSF10C	3.67	3.90	5.46
ZNF167	4.46	6.10	5.88
KIF26B	3.62	4.61	7.68
STRA6	2.26	1.08	6.57

2. match: sample type ("tumor" or "normal") in "exp".

Table2. Identification of tumor sample and normal sample

State	Identification
Normal	TCGA-A6-2671-11A-01R-A32Z-07
Normal	TCGA-A6-2675-11A-01R-1723-07
Tumor	TCGA-A6-2675-01A-02R-1723-07
Normal	TCGA-A6-2678-11A-01R-A32Z-07
Normal	TCGA-A6-2679-11A-01R-A32Z-07
Normal	TCGA-A6-2680-11A-01R-A32Z-07
Normal	TCGA-A6-2682-11A-01R-A32Z-07
Tumor	TCGA-A6-2682-01A-01R-1410-07

Table 1 is an example of "exp" and Table 2 is an example of "match".

Example "exp": gene expression profiles in cholangiocarcinoma from the genomic data commons data portal (https://portal.gdc.cancer.gov/). There are 45 samples (36 tumor and 9 normal samples) and 20,531 genes in "exp". The DEPTH function will output the heterogeneity score for each of the 36 tumor samples as shown in Table 3.

Table 3. heterogeneity score of tumor samples in output data

Samp	heterogeneity score
TCGA-A6-2675-01A-02R-1723-07	2.954321
TCGA-A6-2682-01A-01R-1410-07	4.307523
TCGA-A6-2684-01A-01R-1410-07	3.916457
TCGA-A6-2685-01A-01R-1410-07	2.85864

Installation

You can install the released version of ‘DEPTH’ with:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
    
devtools::install_github("MLi-lab-Bioinformatics-NJUCM/DEPTH/DEPTH")

Examples

exp=read.csv("DEPTH/exp.csv",header=F)
match=read.csv("DEPTH/match.csv")

library(DEPTH)
DEPTH(exp, match)

Citation

Mengyuan Li, Zhilan Zhang, Lin Li, Xiaosheng Wang. An algorithm to quantify intratumor heterogeneity based on alterations of gene expression profiles. Communications Biology 2020, 3(1), 505. DOI: https://doi.org/10.1038/s42003-020-01230-7.