integrateProactiv: Integrate multiple proActiv runs

In GoekeLab/proActiv: Estimate Promoter Activity from RNA-Seq data

Description

Integrate multiple proActiv runs

Usage

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

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 Jan. 30, 2022, 3:52 a.m.