mergeCAGEsets {CAGEr} | R Documentation

## Merge two CAGEr objects into one

### Description

Merges two `CAGEr` objects into one by combining the CTSS genomic coordinates and raw tag counts. The resulting object will contain a union of TSS positions present in the two input objects and raw tag counts for those TSSs in all samples from both input objects.

### Usage

    mergeCAGEsets(cs1, cs2)

    ## S4 method for signature 'CAGEset,CAGEset'
    mergeCAGEsets(cs1, cs2)

    ## S4 method for signature 'CAGEexp,CAGEexp'
    mergeCAGEsets(cs1, cs2)

### Arguments

`cs1` | A `CAGEr` object
`cs2` | A `CAGEr` object

### Value

Note that merging discards all other information present in the two `CAGEr` objects, that is, the merged object will not contain any normalised tag counts, CTSS clusters, quantile positions, etc., so these have to be calculated again by calling the appropriate functions on the merged object. Also, it is only possible to merge two objects that contain TSS information for the same reference genome and do not share any sample names.

Returns a `CAGEset` or `CAGEexp` object, which contains a union of TSS positions present in the two input objects and raw tag counts for those TSSs in all samples from both input objects.

### Author(s)

Vanja Haberle

### See Also

`CAGEset`, `CAGEexp`

### Examples

    library(BSgenome.Drerio.UCSC.danRer7)

    pathsToInputFiles <- system.file("extdata", c("Zf.unfertilized.egg.chr17.ctss",
      "Zf.30p.dome.chr17.ctss", "Zf.prim6.rep1.chr17.ctss"), package="CAGEr")

    myCAGEset1 <- new("CAGEset", genomeName = "BSgenome.Drerio.UCSC.danRer7",
    inputFiles = pathsToInputFiles[1:2], inputFilesType = "ctss", sampleLabels =
    c("sample1", "sample2"))
    getCTSS(myCAGEset1)

    myCAGEset2 <- new("CAGEset", genomeName = "BSgenome.Drerio.UCSC.danRer7",
    inputFiles = pathsToInputFiles[3], inputFilesType = "ctss", sampleLabels =
    "sample3")

    getCTSS(myCAGEset2)

    myCAGEset <- mergeCAGEsets(myCAGEset1, myCAGEset2)

    ce1 <- CAGEexp(genomeName = "BSgenome.Drerio.UCSC.danRer7",
    inputFiles = pathsToInputFiles[1:2], inputFilesType = "ctss", sampleLabels =
    c("sample1", "sample2"))
    getCTSS(ce1)

    ce2 <- CAGEexp(genomeName = "BSgenome.Drerio.UCSC.danRer7",
    inputFiles = pathsToInputFiles[3], inputFilesType = "ctss", sampleLabels =
    "sample3")

    getCTSS(ce2)

    ce <- mergeCAGEsets(ce1, ce2)

[Package CAGEr version 1.22.3 Index]