AtenaParam-class {atena} | R Documentation |
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.
## S4 method for signature 'AtenaParam' path(object) ## S4 method for signature 'AtenaParam' features(object)
object |
A AtenaParam object. |
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.
bfl
A BamFileList object.
features
A GRanges object.
aggregateby
Character vector with column names in the annotation to be used to aggregate quantifications.
ERVmapParam-class
TelescopeParam-class
TEtranscriptsParam-class
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)