DMC_feature: Annotate the differentially methylated cytosine (DMC) to...

In xiaowangCN/GeneDMRs: GeneDMRs: an R package for Gene-based differentially methylated regions analysis

Annotate the differentially methylated cytosine (DMC) to features.

Description

This function annotates the differentially methylated cytosine (DMC) after statistical test Logic_regression() to gene body or CpG island features.

Usage

DMC_feature(
  siteall_significant,
  featureid = TRUE,
  featurefile = list(inputgenebodyfile, inputcpgifeaturefile)
)

Arguments

siteall_significant	refers to the input file with DMC sites.
featureid	refers to whether to include the feature id or not, with the default TRUE. The feature id will output the id of first file of the featurefile list e.g., the id (gene name) of inputgenebodyfile.
featurefile	refers to the input feature files e.g., inputgenebodyfile and inputcpgifeaturefile, with default two files in a list as featurefile = list(inputgenebodyfile, inputcpgifeaturefile), and it can also be one file without a list e.g., featurefile = inputgenebodyfile.

Value

Outputs a data frame contains DMC sites with features.

Examples

siteall_significant_feature <- DMC_feature(siteall_significant, featurefile = list(inputgenebodyfile, inputcpgifeaturefile))
siteall_significant_feature <- DMC_feature(siteall_significant, featureid = FALSE, featurefile = list(inputgenebodyfile, inputcpgifeaturefile))
siteall_significant_feature <- DMC_feature(siteall_significant, featureid = TRUE, featurefile = inputgenebodyfile)

xiaowangCN/GeneDMRs documentation built on Nov. 22, 2023, 11:19 p.m.