dmr: Find the differential methylation regions in the elements of...

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

Description

Find the differential methylation regions or the regions that related with the phenotype who are in the elements of lincRNA etc.

Usage

dmr(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,num,sole=FALSE)

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 regions will be calculated.
contin	If phenotype is continuous,contin is 'ON',and use linear regression to find the regions that related with the phenotype.
testmethod	The method to do the test to find dmr 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	It is the threshold for cutting raw P value.
adjustpcut	It is the threshold for cutting adjust P value.
betadiffcut	The minimum differential between two groups' means while contin is 'OFF'.
num	The number which is the box plot of different methylation regions to plot.
sole	Whether keep the no duplicate records.

Details

dmr is designed to find differential methylation regions or the regions in the elements of lincRNA etc. that related with the continuous phenotype. If contin is 'ON', it 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

dmr will return two txt files that one contains the transcripts' elements and the region of chromosome 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 these significant regions. There are box plot for most significative regions and heat map all significative regions.

Author(s)

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

See Also

See Also dms and dme

Examples

   Dir <- system.file("extdata/localdata",package="LncDM")
   dir.create(paste(Dir,"/dmr",sep=""))
   ###user can set the dir of their own
   setwd(paste(Dir,"/dmr",sep=""))
   ###load the result of loaddata()
   load(paste(Dir,"/loadData.Rdata",sep=""))
   dmr(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,num=1,sole=FALSE)

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