mergeSamples: Merge CAGE samples

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

Description

Merges individual CAGE samples (datasets, experiments) within the CAGEr object into specified groups.

Usage

mergeSamples(object, mergeIndex, mergedSampleLabels)

## S4 method for signature 'CAGEset,numeric'
mergeSamples(object, mergeIndex,
  mergedSampleLabels)

## S4 method for signature 'CAGEexp,ANY'
mergeSamples(object, mergeIndex,
  mergedSampleLabels)

Arguments

object	A CAGEr object.
mergeIndex	Integer vector specifying which experiments should be merged. (one value per sample, see Details).
mergedSampleLabels	Labels for the merged datasets (same length as the number of unique values in mergeIndex)

Details

The samples within the CAGEr object are merged by adding the raw tag counts of individual CTSS that belong tho the same group. After merging, all other slots in the CAGEr object will be reset and any previous data for individual experiments will be removed.

mergeIndex controls which samples will be merged. It is an integer vector that assigns a group identifier to each sample, in the same order as they are returned by sampleLabels(object). For example, if there are 8 CAGE samples in the CAGEr object and mergeIndex = c(1,1,2,2,3,2,4,4), this will merge a) samples 1 and 2, b) samples 3, 4 and 6, c) samples 7 and 8, and d) it will leave sample 5 as it is, resulting in 4 final merged datasets.

Labels provided in mergedSampleLabels will be assigned to merged datasets in the ascending order of mergeIndex values, i.e. first label will be assigned to a dataset created by merging datasets labeled with lowest mergeIndex value (in this case 1), etc.

Value

The slots sampleLabels, librarySizes and tagCountMatrix of the provided CAGEr object will be updated with the information on merged CAGE datasets and will replace the previous information on individual CAGE datasets. All further slots with downstream information will be reset.

Author(s)

Vanja Haberle

Examples

mergeSamples( exampleCAGEset
            , mergeIndex = c(1,1,2)
            , mergedSampleLabels = c("mergedSample1", "mergedSample2"))
exampleCAGEset

mergeSamples( exampleCAGEexp
            , mergeIndex = c(3,2,4,4,1)
            , mergedSampleLabels = c("zf_unfertilized", "zf_high", "zf_30p_dome", "zf_prim6"))
exampleCAGEexp

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