overlapFragWithFeatures {Chicago} | R Documentation

## Overlap Other-Ends with Features

### Description

This function checks which other-ends from a `chicagoData` object overlap with a set of genomic features.

### Usage

    overlapFragWithFeatures(x = NULL, folder = NULL, list_frag, position_otherEnd = NULL,
      sep = "\t")

### Arguments

`x` | a `chicagoData` object or a data table (`data.table`) containining other end IDs.
`folder` | the name of the folder where the files containing the features of interest are stored.
`list_frag` | a list where each element is the name of a file containing a feature of interest (e. g. H3K4me1, CTCF, DHS etc.). These files must have a bed format, with no header. Each element of the list must be named.
`position_otherEnd` | the name of the file containing the coordinates of the restriction fragments and the corresponding IDs. The coordinates should be "chromosome", "start" and "end", and the ID should be numeric. `position_otherEnd` only needs to be specified if x is not a `chicagoData` object.
`sep` | the field separator character. Values are separated by this character on each line of the file containing the coordinates of the restriction fragments (called by `position_otherEnd`).

### Value

a data table (`data.table`) built from `x`, where a column was added for each genomic feature present in `list_frag`. The new columns contain logical values indicating whether there was an overlap or not.

### Author(s)

Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett

### Examples

    data(cdUnitTest)

    ##modifications to cdUnitTest, ensuring it uses correct design directory
    designDir <- file.path(system.file("extdata", package="Chicago"), "unitTestDesign")
    cdUnitTest <- modifySettings(cd=cdUnitTest, designDir=designDir)

    ##get the unit test ChIP tracks
    dataPath <- system.file("extdata", package="Chicago")
    ChIPdir <- file.path(dataPath, "unitTestChIP")
    dir(ChIPdir)

    ##get a list of the unit test ChIP tracks
    featuresFile <- file.path(ChIPdir, "featuresmESC.txt")
    featuresTable <- read.delim(featuresFile, header=FALSE, as.is=TRUE)
    featuresList <- as.list(featuresTable$V2)
    names(featuresList) <- featuresTable$V1

    ##test for overlap
    overlapFragWithFeatures(cdUnitTest, folder=ChIPdir, list_frag = featuresList)

[Package Chicago version 1.15.0 Index]