pairwiseRegions: Classify two Binding Profiles

In SimBindProfiles: Similar Binding Profiles

Description

Classify two Binding Profiles into unique and common binding regions and write results to bed files.

Usage

pairwiseRegions(xSet, sgrset = c(1, 2), bound.cutoff, diff.cutoff, probes, probe.max.spacing, writeBedFile=TRUE)

Arguments

xSet	object of class ExpressionSet
sgrset	vector of lenght 2; specifying which data sets to compare from the ExpressionSet
bound.cutoff	numeric; threshold above probes are considered “bound”
diff.cutoff	numeric; difference threshold to determine if object 1 and object 2 are unqiquely bound
probes	integer; minimum number of probes in a valid region
probe.max.spacing	integer; maximum number of base pairs in a gap before splitting a region into 2 regions
writeBedFile	logical; should bed file be written

Details

Probe signal values above the bound.cutoff in both data are classified as common bound. Probes which are above the bound.cutoff and in one data and higher than the diff.cutoff to the other data are called unique. Then these probes are then filtered into regions using the probes and probe.max.spacing details. The score for the unique regions is calculated as mean (probes in region set 1 minus set 2), or vise versa. The score for the common region is the mean (probes in region (set 1 plus set 2)/2). Optional bed file formated result files are written using the choosen options in the file names.

Value

data.frame with the following columns:

name	name(s) of data set to which region belongs
class.group	class group; 1, 2 or 3 for common regions between both sets
chr	chromsome
start	start position of region
end	end position of region
scrore	score of region
nProbes	number of probes in region

Author(s)

Bettina Fischer, Robert Stojnic

See Also

compensationRegions, increasedBindingRegions, threewayRegions

Examples

  dataPath <- system.file("data",package="SimBindProfiles")
  load(file.path(dataPath,"SGR.RData"))
  pairAB <- pairwiseRegions(SGR, sgrset=c(1,2), bound.cutoff=1.86, diff.cutoff=1.4, 
            probes=10, probe.max.spacing=200)

SimBindProfiles documentation built on Nov. 8, 2020, 5:57 p.m.