computeDiffTab.default.region {RnBeads} | R Documentation

## 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

### Author(s)

Fabian Mueller

### 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)

[Package RnBeads version 1.12.1 Index]