outputDMfunc {IMA}R Documentation

Output the differentially methylated sites/regions

Description

This function will output the differential testing results with user-specified significance criteria.

Usage

outputDMfunc(out, rawpcut = 0.05, adjustpcut = 0.05, betadiffcut = 0.14)

Arguments

out

This is the output by function of sitetest, testfunc or regionwrapper with three columns for each site/region: p-value, adjusted p-value and β value difference.

rawpcut

either null or define the output cut-off for the raw p-value

adjustpcut

either null or define the output cut-off for the adjusted p-value

betadiffcut

either null or define the output cut-off for the β value difference between two groups.

Value

return a matrix with "P-Value", "Adjust Pval","beta-Difference" in separate columns for each site/region satisfying the specified significance criteria.

Author(s)

Dan Wang, Li Yan, Qiang Hu, Dominic J Smiraglia, Song Liu

Maintainer: Dan Wang <wangdan412@gmail.com>

See Also

IMA.methy450R,regionswrapper,IMA.methy450PP,testfunc,indexregionfunc

Examples

# > sitetest = sitetest(dataf,gcase="g2",gcontrol="g1",testmethod = "mean",
# + Padj="BH",rawpcut = NULL,adjustpcut =NULL,betadiffcut = NULL)
# > sitetest = outputDMfunc(sitetest,rawpcut = 0.05,adjustpcut =0.05,
# + betadiffcut = 0.14)
### The list of loci with adjusted p-value less than 0.05 and beta value 
### difference at least 0.14 will be outputted

[Package IMA version 3.1.2 Index]