GEO_EstimateMissingValues_Methylation: The GEO_EstimateMissingValues_Methylation function

View source: R/GEO_Download_Preprocess.R

GEO_EstimateMissingValues_MethylationR Documentation

The GEO_EstimateMissingValues_Methylation function

Description

Internal. Removes samples and probes with more missing values than the MissingValueThreshold, and imputes remaining missing values using Tibshirani's KNN method.

Usage

GEO_EstimateMissingValues_Methylation(
  MET_Data,
  MissingValueThresholdGene = 0.3,
  MissingValueThresholdSample = 0.3
)

Arguments

MET_Data

methylation data or gene expression data matrix.

MissingValueThresholdGene

threshold for missing values per gene. Genes with a percentage of NAs greater than this threshold are removed. Default is 0.3.

MissingValueThresholdSample

threshold for missing values per sample. Samples with a percentage of NAs greater than this threshold are removed. Default is 0.1.

Value

the dataset with imputed values and possibly some genes or samples deleted.


gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.