filterLinearProbes: The filterLinearProbes function

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

The filterLinearProbes function

Description

use a linear regression filter to screen for probes that were negatively associated with gene expression.

Usage

filterLinearProbes(
  methylation.data,
  gene.expression.data,
  ProbeAnnotation,
  cores,
  filter,
  cluster,
  correlation = "negative"
)

Arguments

methylation.data	methylation data matrix.
gene.expression.data	gene expression data matrix.
ProbeAnnotation	dataframe of probe annotation
cores	number of CPU cores used for computation
filter	logical indicating whether to perform a linear regression to select functional probes
cluster	logical indicating whether the CpGs were clustered using hierarchical clustering
correlation	Character vector indicating the expected correlation between DNA methylation and gene expression. Can be either 'negative' or 'positive'. Default: 'negative'.

Value

a character vector of probe names.

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