Find the differential methylation regions in the elements of lincRNA, protein coding gene ,processed transcript and pseudogene

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Description

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

Usage

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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 Zhizhihui013201@gmail.com,Yanxun Suhmu_yanxunsu@163.com,Xin Lilixin920126@163.com

See Also

See Also dms and dme

Examples

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   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)