increasedBindingRegions: Classify two Binding Profiles - Increased Binding

In SimBindProfiles: Similar Binding Profiles

Description

This function is used to classify two Binding Profiles into regions which are more bound in one data set than the other.

Usage

increasedBindingRegions(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 uniquely 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 a bed file be written

Details

Probe signal values above the bound.cutoff threshold for both data sets are compared where set 1 is above the diff.cutoff of set 2. These probes are then filtered into regions using the probes and probe.max.spacing details. The score is calculated as mean (probes in region set 1 minus set 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, in this case only 1
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

pairwiseRegions, compensationRegions, threewayRegions, plotBoundProbes

Examples

  dataPath <- system.file("data",package="SimBindProfiles")
  load(file.path(dataPath,"SGR.RData"))
  overcompBC <- increasedBindingRegions(SGR, sgrset=c(2,3), 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.