QuantifyParam-class: QuantifyParam parameter class

In functionalgenomics/atena: Analysis of Transposable Elements

QuantifyParam 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 'QuantifyParam'
path(object)

## S4 method for signature 'QuantifyParam'
features(x)

Arguments

object	A QuantifyParam object.
x	A QuantifyParam 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.

ovMode

Character vector indicating the overlapping mode. Available options are: "ovUnion" (default) and "ovIntersectionStrict", which implement the corresponding methods from HTSeq (https://htseq.readthedocs.io/en/release_0.11.1/count.html). In the TEtranscripts, ERVmap and Telescope methods ambiguous alignments (alignments overlapping > 1 feature) are addressed differently depending on the method. In the atena method, those overlaps are not counted.

See Also

ERVmapParam-class TelescopeParam-class TEtranscriptsParam-class atenaParam-class

Examples

bamfiles <- list.files(system.file("extdata", package="atena"),
                       pattern="*.bam", full.names=TRUE)
## Not run: 
## use the following two instructions to fetch annotations, they are here
## commented out to enable running this example quickly when building and
## checking the package
rmskat <- annotaTEs(genome="dm6", parsefun=rmskatenaparser,
                    strict=FALSE, insert=500)
rmskLTR <- getLTRs(rmskat, relLength=0.8,
                   fullLength=TRUE,
                   partial=TRUE)

## End(Not run)

## DO NOT TYPE THIS INSTRUCTION, WHICH JUST LOADS A PRE-COMPUTED ANNOTATION
## YOU SHOULD USE THE INSTRUCTIONS ABOVE TO FETCH ANNOTATIONS
rmskLTR <- readRDS(system.file("extdata", "rmskatLTRrlen80flenpartoth.rds",
                               package="atena"))

## build a parameter object for TEtranscripts
ttpar <- TEtranscriptsParam(bamfiles,
                            teFeatures=rmskLTR,
                            singleEnd=TRUE,
                            ignoreStrand=TRUE)
## just check that the parameter object belongs to the expected classes
is(ttpar, "QuantifyParam")
is(ttpar, "TEtranscriptsParam")

functionalgenomics/atena documentation built on Nov. 4, 2024, 7:33 p.m.