AtenaParam-class {atena}

R Documentation

Atena parameter class

Description

This is a virtual class from which other classes are derived for storing parameters provided to quantification methods of transposable elements from RNA-seq data.

Usage

## S4 method for signature 'AtenaParam'
path(object)

## S4 method for signature 'AtenaParam'
features(object)

Arguments

object

A AtenaParam object.

Value

path(): Filesystem paths to the BAM files in the input parameter object.

features(): The GenomicRanges or GenomicRangesList object with the features in the input parameter object.

Slots

bfl

A BamFileList object.

features

A GRanges object.

aggregateby

Character vector with column names in the annotation to be used to aggregate quantifications.

See Also

ERVmapParam-class TelescopeParam-class TEtranscriptsParam-class

Examples

bamfiles <- list.files(system.file("extdata", package="atena"),
                       pattern="*.bam", full.names=TRUE)
TE_annot <- readRDS(file = system.file("extdata", "Top28TEs.rds",
                    package="atena"))
ttpar <- TEtranscriptsParam(bamfiles, teFeatures=TE_annot, singleEnd=TRUE,
                            ignoreStrand=TRUE, aggregateby = c("repName"))
path(ttpar)

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