mergeExp: Merge splicing variant expression from multiple samples

In casper: Characterization of Alternative Splicing based on Paired-End Reads

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

casper documentation built on Dec. 17, 2020, 2:01 a.m.