MEDIPS.selectROIs: Selects row-wise subsets of a result table as returned by the...

In HPCBio/MEDIPS-BioC: DNA IP-seq data analysis

Description

MEDIPS provides the functionality to select subsets of the result matrix returned by the MEDIPS.meth function according to any given set of regions of interest (ROIs).

Usage

MEDIPS.selectROIs(results=NULL, rois=NULL, columns=NULL, summarize=NULL)

Arguments

results	a result table as returned by the function MEDIPS.meth
rois	A matrix containing genomic coordinates of any regions of interest.
columns	Only selected columns will be returned as determined by the columns parameter. It is possible to specify one or more concrete column names, please see an example below.
summarize	By setting summarize=NULL (default) all windows included in the genomic ranges of the given ROIs will be returned. As an alternative, it is possible to calculate mean (summarize = "avg") or sum (summarize = "sum") values over the individual windows included in each ROI, or to select only the most significant window within each given ROI (summarize="minP").

Author(s)

Lukas Chavez, Matthias Lienhard

Examples

library(MEDIPSData)
data(resultTable)

rois=data.frame(chr=c("chr22","chr22"), start=c(19136001, 19753401), stop=c(19136200, 19753500), ID=c("ID_1", "ID_2"))
columns=names(resultTable)[grep("counts|rpkm|logFC",names(resultTable))]
s = MEDIPS.selectROIs(results=resultTable, rois=rois, columns=columns, summarize=NULL)

HPCBio/MEDIPS-BioC documentation built on May 30, 2019, 12:44 p.m.