regionLevel: Calculate the beta values of elements in lincRNA etc

In LncDM: The Different Methylation Sites, Elements and Regions of lncRNA

Description

Calculate the beta values of elements in lincRNA etc. based on reannotation information.

LincRNA and processed transcript's elements are TSS1500, TSS200, 1_exon, genebody and intron. Protein coding gene and pseudogene transcript's elements are 5'UTR, 3'UTR, TSS1500, TSS200, 1_exon, genebody and intron.

Usage

regionLevel(data,indexmethod = c("mean", "median"),classes=c("gene","lincRNA",
"processed_transcript","pseudogene"))

Arguments

data	The objects of class LincMethy450 which return from loaddata. The beta matrix of sites. A site per row and A sample per column.
indexmethod	The method to calculate the beta if there are more than two CpG sites in a element.
classes	Whose CpG sites will be calculated.

Details

The function, regionLevel, is designed to calculate the beta value of gene, lincRNA, processed_transcript and pseudogenes' elements. If indexmethod is "mean" ,and the mean of CpG sites' beta value will be regarded as the element's beta. If classes is "gene", only the elements of protein coding genes' transcript will be calculated. If want to calculate more than one class, please do it respectively.

Value

This methods will return a object of class RegionMethy450. It contains some matrix of elements' beta values. A row per transcript, a col per sample.

Author(s)

Hui [e-mail],Yanxun [e-mail],Xin [e-mail]

See Also

See Also dms, dme and dmr

Examples

## Not run: 
  Dir <- system.file("extdata/localdata",package="LncDM")
  setwd(Dir)
  ###load the result of loaddata()
  #load(paste(Dir,"/loadData.Rdata",sep=""))
  Region <- regionLevel(data=loadData,indexmethod = "mean",classes="lincRNA")
  ###save the region data in order to caculate dme
  save(Region,file="Region.Rdata")

## End(Not run)

LncDM documentation built on May 2, 2019, 6:09 p.m.