SimBindProfiles (version 1.10.0)

increasedBindingRegions: Classify two Binding Profiles - Increased Binding

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

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

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.

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)