View source: R/GetSampleDMFun.R
GetSampleDMFun | R Documentation |
This function computes sample-specific DM genes for each sample. It computes M-values from gene-centric beta values and computes the median of gene-centric M-values across all the samples. It considers a gene hypermethylated if the M-value fold-change ≥ 4 and hypomethylated if fold-change ≤ -4.
GetSampleDMFun( DNAmethylation_data, parallel = c("TRUE", "FALSE"), ncores = 2, CTDDirectory = "~" )
DNAmethylation_data |
A R dataframe with gene-centric DNA methylation beta values of bulk tumor samples. Rows are the genes, columns are the tumor samples. |
parallel |
A boolean value ('TRUE' or 'FALSE')indicating if the users want to run this function in multi-core. |
ncores |
An integer value for the number of cores. |
CTDDirectory |
A character string for the file path of the directory for the output to be stored. |
Created By: Banabithi Bose| Date Created: 4/10/2022 | Stage 4 | Function 1 |
R dataframe objects each with a single column containing DM genes for each tumor sample. The column is labeled as gene.
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