increasedBindingRegions {SimBindProfiles} | R Documentation

## 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

### 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)

[Package SimBindProfiles version 1.20.0 Index]