addCor {sevenC} | R Documentation

## Add correlation of ChIP-seq coverage to motif pairs.

### Description

This function first adds ChIP-seq signals along all regions of motif location using the function `addCovToGR`. Than it calculates the correlation of coverage for each input pair using the function `addCovCor`. The Pearson correlation coefficient is added as new metadata column to the input interactions. Note, this function does not work on windows because reading of bigWig files is currently not supported on windows.

### Usage

    addCor(gi, bwFile, name = "chip", window = 1000, binSize = 1)

### Arguments

`gi` | `GInteractions` object.
`bwFile` | File path or connection to BigWig file with ChIP-seq signals.
`name` | Character indicating the sample name.
`window` | Numeric scalar for window size around the center of ranges in `gr`.
`binSize` | Integer scalar as size of bins to which the coverage values are combined.

### Value

An `GInteractions` object like `gi` with a new metadata column `colname` holding Pearson correlation coefficient of ChIP-seq signals for each anchor pair.

### Examples

    if (.Platform$OS.type != "windows") {

     # use example bigWig file of ChIP-seq signals on human chromosome 22
     exampleBigWig <- system.file("extdata",
     "GM12878_Stat1.chr22_1-30000000.bigWig", package = "sevenC")

     # use example CTCF moitf location on human chromosome 22
     motifGR <- sevenC::motif.hg19.CTCF.chr22

     # build candidate interactions
     gi <- prepareCisPairs(motifGR)

     # add ChIP-seq signals correlation
     gi <- addCor(gi, exampleBigWig)

     # use an alternative metadata column name for ChIP-seq correlation
     gi <- addCor(gi, exampleBigWig, name = "Stat1")

     # add ChIP-seq correlation for signals signals in windows of 500bp around
     # motif centers
     gi <- addCor(gi, exampleBigWig, window = 500)

     # add ChIP-seq correlation for signals in bins of 10 bp
     gi <- addCor(gi, exampleBigWig, binSize = 10)

    }

[Package sevenC version 1.12.0 Index]