RnBeads (version 1.4.0)

computeDiffTab.default.region: computeDiffTab.region

Description

computes a difference table containing multiple difference measures, In the simple version the mean of the difference in means, the mean quotient in means and a combination of p-values on the site level are computed. This is computed for each row of the input table. The extended version contains additional columns

Usage

computeDiffTab.default.region(dmtp, regions2sites, includeCovg = FALSE)

Arguments

dmtp

differential methylation table on the site level (as obtained from computeDiffTab.default.site)

regions2sites

a list containing for each region the indices of the corresponding sites in the site differential methylation table

includeCovg

flag indicating whether to include coverage information

Value

a dataframe containing the following variables for a given genomic region:

mean.mean.g1,mean.mean.g2

mean of mean methylation levels for group 1 and 2 across all sites in a region

mean.mean.diff

Mean difference in means across all sites in a region

mean.mean.quot.log2

Mean quotient in means across all sites in a region

comb.p.val

Combined p-value using a generalization of Fisher's method. See combineTestPvalsMeth for details.

comb.p.adj.fdr

FDR adjusted combined p-value

num.sites

number of sites that were considered for a region

mean.num.na.g1/2

mean number (accross all considered sites) of samples that contained an NA for group 1 and 2 respectively

mean.mean.covg.g1/2

Mean value of mean coverage values (across all samples in a group) across all sites in a region

mean.nsamples.covg.thresh.g1/2

mean number (accross all considered sites) of samples that have a coverage larger than the specified threshold (see computeDiffTab.default.site for details) for group 1 and 2 respectively

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
meth.mat <- meth(rnb.set.example)
sample.groups <- rnb.sample.groups(rnb.set.example)[[1]]
dm.sites <- computeDiffTab.extended.site(meth.mat,sample.groups[[1]],sample.groups[[2]])
map.regions.to.sites <- regionMapping(rnb.set.example,"promoters")
dm.promoters <- computeDiffTab.default.region(dm.sites,map.regions.to.sites)