Methmean_region: Calculate the methylation mean for regions.

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

Calculate the methylation mean for regions.

Description

This function outputs the methylation mean for different groups based on gene and CpG island regions by matching with cytosine. It is also for gene body of promoter, exon, intron and TSSes regions, cgpi feature of CpG island and CpG island shores and their interactive regions e.g., promoter CpG island.

Usage

Methmean_region(
  inputmethfile_QC,
  inputrefseqfile,
  cpgifeaturefile = NULL,
  chrnum = "all",
  posistart = NULL,
  posiend = NULL,
  featureid = NULL,
  featurename = NULL
)

Arguments

inputmethfile_QC	refers to the input of methylation file after quality control.
inputrefseqfile	refers to the input file with regions e.g., inputrefseqfile/inputcpgifile with 4 columns or inputgenebodyfile/inputcpgifeaturefile with 5 columns.
cpgifeaturefile	refers to the input of CpG island feature file e.g., inputcpgifeaturefile, with default NULL. If provided, the output file is methylation mean of inputrefseqfile or inputgenebodyfile with CpG island and CpG island shore features.
chrnum	refers to the chromosome number or all chromosomes (all) or all chromosomes with unannotated sites (alls), with default "all".
posistart	refers to start position if requested, with default NULL.
posiend	refers to end position if requested, with default NULL.
featureid	refers to NCBI ID of specific gene or all the genes, with default NULL. The CpG id can also be used like "cpgi1" or "shore2".
featurename	refers to different gene body features of promoter, exon, intron and TSSes. The CpG island features can also be used that are "CpGisland" and "Shores".

Value

Outputs a data frame of the methylation mean of provided regions with/without different features.

Examples

Methmean_region(inputmethfile_QC, inputrefseqfile, chrnum = "alls", featureid = c("NM_001244353", "NM_001244864")) # find sepecific gene by NCBI ID #

Methmean_region(inputmethfile_QC, inputrefseqfile, chrnum = "chr1", posistart = 21800, posiend = 21900)
regiongenechr <- Methmean_region(inputmethfile_QC, inputrefseqfile, chrnum = c("chr1","chr2"))
regiongeneall <- Methmean_region(inputmethfile_QC, inputrefseqfile, chrnum = "all")
DMC_regiongeneall <- Methmean_region(DMC_inputmethfile_QC, inputrefseqfile, chrnum = "all") # Calculate DMC first and then recalculate the methylation mean by replacing the RRBS cytosine sites #
regiongenealls <- Methmean_region(inputmethfile_QC, inputrefseqfile, chrnum = "alls") # alls include unannotated CpG site like chrUn_NW_018084826v1 #
Methmean_region(inputmethfile_QC,inputcpgifile,"chr1", posistart = 21800, posiend = 21900) # acturally regiongenepart = regioncpgpart #
regioncpgchr <- Methmean_region(inputmethfile_QC, inputcpgifile, chrnum = c("chr1","chr2"))
regioncpgall <- Methmean_region(inputmethfile_QC, inputcpgifile, chrnum = "all")
regioncpgalls <- Methmean_region(inputmethfile_QC, inputcpgifile, chrnum = "alls")

regiongenebodychr <- Methmean_region(inputmethfile_QC, inputgenebodyfile, chrnum = c("chr1","chr2"))
regiongenebodyall <- Methmean_region(inputmethfile_QC, inputgenebodyfile, chrnum = "all")
regiongenebodyalls <- Methmean_region(inputmethfile_QC, inputgenebodyfile, chrnum = "alls")
regioncpgifeaturechr <- Methmean_region(inputmethfile_QC, inputcpgifeaturefile, chrnum = c("chr1","chr2"))
regioncpgifeatureall <- Methmean_region(inputmethfile_QC, inputcpgifeaturefile, chrnum = "all")
regioncpgifeaturealls <- Methmean_region(inputmethfile_QC, inputcpgifeaturefile, chrnum = "alls")

partgenebody <- Methmean_region(inputmethfile_QC, inputgenebodyfile, featureid = "NM_001244353")
partgenebodyexon <- Methmean_region(inputmethfile_QC, inputgenebodyfile, featureid = "NM_001244353", featurename = "exons")
partgenebodyall <- Methmean_region(inputmethfile_QC, inputgenebodyfile, featureid = "NM_001244353", featurename = c("promoters","exons","introns","TSSes"))
genebodypromoterall <- Methmean_region(inputmethfile_QC, inputgenebodyfile, featureid = "all", featurename = "promoters")
genebodyexonall <- Methmean_region(inputmethfile_QC, inputgenebodyfile, featureid = "all", featurename = "exons")
genefeatureall <- Methmean_region(inputmethfile_QC, inputgenebodyfile, featureid = "all", featurename = c("promoters","exons","introns","TSSes")) #long time #
partcpgi <- Methmean_region(inputmethfile_QC, inputcpgifeaturefile, featureid = "cpgi1")
partshore <- Methmean_region(inputmethfile_QC, inputcpgifeaturefile, featureid = "shore10")
cpgislandall <- Methmean_region(inputmethfile_QC, inputcpgifeaturefile, featureid = "all", featurename = "CpGisland")
cpgshoreall <- Methmean_region(inputmethfile_QC, inputcpgifeaturefile, featureid = "all", featurename = "Shores") #long time #
cpgfeatureall <- Methmean_region(inputmethfile_QC, inputcpgifeaturefile, featureid = "all", featurename = c("CpGisland", "Shores")) #long time #

genebodychr_promoter <- Methmean_region(inputmethfile_QC, inputgenebodyfile, chrnum = "chr1", featureid = "all", featurename = "promoters")
cpgchr_island <- Methmean_region(inputmethfile_QC, inputcpgifeaturefile, chrnum = "chr1", featureid = "all", featurename = "CpGisland")

# when the cpgifeaturefile = inputcpgifeaturefile is provided #
regiongenechr_cpgfeature <- Methmean_region(inputmethfile_QC, inputrefseqfile, cpgifeaturefile = inputcpgifeaturefile, chrnum = c("chr1","chr2"))
regiongeneall_cpgfeature <- Methmean_region(inputmethfile_QC, inputrefseqfile, cpgifeaturefile = inputcpgifeaturefile, chrnum = "all")
regiongenealls_cpgfeature <- Methmean_region(inputmethfile_QC, inputrefseqfile, cpgifeaturefile = inputcpgifeaturefile, chrnum = "alls")
genebodypromoterall_cpgfeature <- Methmean_region(inputmethfile_QC, inputgenebodyfile, cpgifeaturefile = inputcpgifeaturefile, featureid = "all", featurename = "promoters")
genebodyexonall_cpgfeature <- Methmean_region(inputmethfile_QC, inputgenebodyfile, cpgifeaturefile = inputcpgifeaturefile, featureid = "all", featurename = "exons")
genefeatureall_cpgfeature <- Methmean_region(inputmethfile_QC, inputgenebodyfile, cpgifeaturefile = inputcpgifeaturefile, featureid = "all",
featurename = c("promoters","exons","introns","TSSes")) #long time #

# windows #
windowfileall <- Methmean_region(inputmethfile_QC, windowfile, chrnum = "all")
windowfilealls <- Methmean_region(inputmethfile_QC, windowfile, chrnum = "alls")

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