integrateProactiv: Integrate multiple proActiv runs

Description Usage Arguments Value Examples

View source: R/proActiv.R

Description

Integrate multiple proActiv runs

Usage

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integrateProactiv(res1, res2, ..., promoterAnnotation, renormalize = TRUE)

Arguments

res1

A summarizedExperiment object returned by proActiv

res2

A summarizedExperiment object returned by proActiv

...

Additional summarizedExperiment objects returned by proActiv

promoterAnnotation

Promoter annotation object used to create proActiv runs

renormalize

Whether to renormalize counts after merging. Defaults to TRUE

Value

A SummarizedExperiment object with assays giving promoter counts and activity with gene expression. rowData contains promoter metadata and absolute promoter activity summarized across conditions (if condition is provided)

Examples

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f1 <- list.files(system.file('extdata/vignette/junctions', 
                             package = 'proActiv'), 
                 full.names = TRUE, pattern = 'A549')
f2 <- list.files(system.file('extdata/vignette/junctions', 
                             package = 'proActiv'), 
                 full.names = TRUE, pattern = 'HepG2')
promoterAnnotation <- promoterAnnotation.gencode.v34.subset
res1 <- proActiv(files = f1, promoterAnnotation  = promoterAnnotation,
                 condition = rep('A549',3))
res2 <- proActiv(files = f2, promoterAnnotation = promoterAnnotation,
                 condition = rep('HepG2',3))
res <- integrateProactiv(res1, res2, promoterAnnotation = promoterAnnotation)

GoekeLab/proActiv documentation built on June 26, 2021, 6:39 a.m.