mergeCAGEsets: Merge two CAGEr objects into one

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

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)

CAGEr documentation built on Jan. 17, 2021, 2 a.m.