mergeExp {casper} | R Documentation

## Merge splicing variant expression from multiple samples

### Description

`mergeExp` combines the output of `calcExp` from multiple samples, i.e. multiple `ExpressionSet` objects, into a single `ExpressionSet`

### Usage

    mergeExp(..., sampleNames,  keep=c('transcript','gene_id','island_id'))

### Arguments

`...` | `ExpressionSet` objects to be combined.
`sampleNames` | Character vector indicating the name of each sample. Defaults to 'Sample1', 'Sample2', etc.
`keep` | Variables in the featureData of each individual `ExpressionSet` to keep in the merged output.

### Details

`mergeExp` runs some checks to ensure that object can be combined (e.g. making sure that measurements are obtained on same set of genes), then sorts and formats each input `ExpressionSet`.

A label with the sample name is appended to variables in the featureData that appear in multiple samples, e.g. variable 'se' reporting standard errors (obtained by setting citype='asymp' in calcExp).

### Value

Object of class `ExpressionSet` combining the input ExpressionSets. Its `featureData` contains the columns indicated in the keep argument, plus a column `readCount` with the total number of reads mapped to each gene (or gene island, when multiple genes have overlapping exons).

### Author(s)

David Rossell

### See Also

`calcExp` to obtain an `ExpressionSet` for an individual sample.

### Examples

    #See example in calcExp

[Package casper version 2.20.0 Index]