dms: Find the differential methylation CpG sites in the lincRNA,...

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

Description

Find the differential methylation sites or the sites that related with the phenotype who are in the lincRNA etc.

Usage

dms(data,contin=c("ON","OFF"),classes=c("lincRNA","gene","processed_transcript",
"pseudogene"),testmethod = c("wilcox","limma", "t.test", "satterthwaite"), Padj =
c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"), gcase =
"case", gcontrol = "control", paired = FALSE,rawpcut = 0.05, adjustpcut = 0.05,
 betadiffcut = 0.3,XY=c(FALSE,"X","Y",c("X","Y")),tlog=FALSE,num)

Arguments

data	The objects of class LincMethy450 which return from loaddata. The beta matrixs of sites. A site per row and A sample per column.
classes	Whose CoG sites will be calculated
contin	If phenotype is continuous,contin is 'ON',and use linear regression to find the sites that related with the phenotype.
testmethod	The method to do the test to find dms while contin is 'OFF' which means phenotype is discontinuous.
Padj	The method of multiple testing adjustment to adjust P value.
gcase	The name of case group while contin is 'OFF'.
gcontrol	The name of case group while contin is 'OFF'.
paired	Whether compare in pairs while do t.test.
rawpcut	The threshold for cutting raw P value.
adjustpcut	The threshold for cutting adjust P value.
betadiffcut	The minimum differential between two groups' means while contin is 'OFF'.
num	The number of sites,elements or regions to plot.
XY	The chromosomes that where CpG sites were filtered.
tlog	Whether do the log transform for the P values.

Details

dms is designed to find differential methylation sites or the CpG sites that related with the continuous phenotype. If contin is 'ON', which means the phenotype is continuous, and linear regression will be used. If the phenotype isn't continuous, test such as t test will be used.

Value

dms will return two txt files that one contains the sites whose P value less than rawpcut, adjust P less than adjustpcut and the differ of the means of two groups more than betadiffer while another is the beta matrix of dms. There are box plot for most significative sites,heat map and Manhattan of all significative sites.

Author(s)

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

See Also

See Also dme and dmr

Examples

   Dir <- system.file("extdata/localdata",package="LncDM")
   dir.create(paste(Dir,"/dms",sep=""))
   ###user can set the dir of their own
   setwd(paste(Dir,"/dms",sep=""))
   ###load the result of loaddata()
   load(paste(Dir,"/loadData.Rdata",sep=""))
   dms(data=loadData,contin="OFF",classes="lincRNA",testmethod = "t.test", Padj = "fdr", 
   gcase = "case", gcontrol = "control", paired = FALSE,rawpcut = 0.05, adjustpcut = 0.05, 
   betadiffcut = 0.3,XY=c(FALSE,"X","Y"),tlog=FALSE,num=1)

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