RunDeconvExprFun: Deconvolution of gene expression of bulk tumor samples

In bozdaglab/CTDPathSim2.0: Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

Deconvolution of gene expression of bulk tumor samples

Description

This function utilizes the estimated cell proportions from Step 1 as a fixed input and computes an average gene expression profiles of constituent cell types through a constrained least-squares using quadratic programming.

Usage

RunDeconvExprFun(Expression.Sample, Deconv_proportions)

Arguments

Expression.Sample	A R dataframe for the gene-centric gene expression (RNASeq) values of the tumor samples.
Deconv_proportions	A R dataframe with estimated cell proportions in tumor samples from output of the RunDeconvMethylFun() function.

Details

Created By: Banabithi Bose| Date Created: 4/10/2022 | Stage 2 | Function 1 |

Value

A R dataframe with gene expression values in constituent cell types. The rows are the genes and the columns are the cell types. This function labels the columns as ,1, ,2,,3,....etc.

bozdaglab/CTDPathSim2.0 documentation built on April 14, 2022, 12:39 a.m.