integrateProactiv {proActiv} | R Documentation

## Integrate multiple proActiv runs

### 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)

[Package proActiv version 1.4.0 Index]