Significant_filter: Filter the significant regions or cytosine sites.

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

Filter the significant regions or cytosine sites.

Description

This function filters significant regions or cytosine sites based on Q value and methylation difference.

Usage

Significant_filter(
  genefeatureall_cpgfeature_Qvalue,
  qvalue = 0.01,
  methdiff = 0,
  featureout = 1
)

Arguments

genefeatureall_cpgfeature_Qvalue	refers to the input file with Q values and methylation differences need to be filtered.
qvalue	refers to the threshold of Q values that Q values larger than this will be discarded, with default 0.01.
methdiff	refers to the threshold of methylation differences that methylation differences less than this will be discarded, with the default 0.
featureout	refers to which feature will be filtered, with default 1. When featureout = 2, it means that the second feature will be filtered and outputted.

Value

Outputs a data frame of the significant regions or cytosine sites.

Examples

genefeatureall_cpgfeature_significantcpgisland <- Significant_filter(genefeatureall_cpgfeature_Qvalue)
genefeatureall_cpgfeature_significantshore <- Significant_filter(genefeatureall_cpgfeature_Qvalue, featureout = 2)
genefeatureall_cpgfeature_significantcpgisland <- Significant_filter(genefeatureall_cpgfeature_Qvalue, qvalue = 0.001, methdiff = 0.01, featureout = 1)
regiongeneall_cpgfeature_significantcpgisland <- Significant_filter(regiongeneall_cpgfeature_Qvalue, methdiff = 0.05, featureout = 1)
regiongeneall_significant <- Significant_filter(regiongeneall_Qvalue)
regiongenealls_significant <- Significant_filter(regiongenealls_Qvalue, methdiff = 0.05)
siteall_significant <- Significant_filter(siteall_Qvalue)
siteall_significant <- Significant_filter(siteall_Qvalue, qvalue = 0.001, methdiff = 0.1)

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