MEDIPS.selectROIs {MEDIPS} | R Documentation |
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).
MEDIPS.selectROIs(results=NULL, rois=NULL, columns=NULL, summarize=NULL)
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"). |
Lukas Chavez, Matthias Lienhard
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)