GetCellLineDMFun: Cell line-specific differentially (DM) genes

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

Cell line-specific differentially (DM) genes

Description

This function computes cell line-specific DM genes for each cell lines It computes M-values from gene-centric beta values and computes the median of gene-centric M-values across all the cell lines It considers a gene hypermethylated if the M-value fold-change ≥ 4 and hypomethylated if fold-change ≤ -4.

Usage

GetCellLineDMFun(
  DNAmethylation_data,
  parallel = c("TRUE", "FALSE"),
  ncores = 2,
  CTDDirectory = "~"
)

Arguments

DNAmethylation_data	A R dataframe with gene-centric DNA methylation beta values of cell lines. Rows are the genes, columns are the cell lines.
parallel	A boolean value ('TRUE' or 'FALSE')indicating if the users want to run this function in multi-core.
ncores	A integer value for the number of cores.
CTDDirectory	A character string for the file path of the directory for the output to be stored.

Details

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

Value

R dataframe objects each with a single column containing DM genes for each cell line. The column is labeled as gene.

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