qtex: Quantify transposable element expression

In functionalgenomics/atena: Analysis of Transposable Elements

Quantify transposable element expression

Description

The qtex() method quantifies transposable element expression.

Usage

## S4 method for signature 'ERVmapParam'
qtex(
  x,
  phenodata = NULL,
  mode = ovUnion,
  yieldSize = 1000000L,
  verbose = 1,
  BPPARAM = SerialParam(progressbar = ifelse(verbose == 1, TRUE, FALSE))
)

## S4 method for signature 'TEtranscriptsParam'
qtex(
  x,
  phenodata = NULL,
  mode = ovUnion,
  yieldSize = 1000000L,
  BPPARAM = SerialParam(progressbar = TRUE)
)

## S4 method for signature 'TelescopeParam'
qtex(
  x,
  phenodata = NULL,
  mode = ovUnion,
  yieldSize = 1000000L,
  auxiliaryFeatures = FALSE,
  BPPARAM = SerialParam(progressbar = TRUE)
)

## S4 method for signature 'atenaParam'
qtex(
  x,
  phenodata = NULL,
  mode = ovUnion,
  yieldSize = 1000000L,
  auxiliaryFeatures = FALSE,
  BPPARAM = SerialParam(progressbar = TRUE)
)

Arguments

x	An QuantifyParam object of one of the following subclasses: A TEtranscriptsParam object built using the constructor function TEtranscriptsParam(). This object will trigger qtex() to use the quantification algorithm by Jin et al. (2015). A ERVmapParam object built using the constructor function ERVmapParam(). This object will trigger qtex() to use the quantification algorithm by Tokuyama et al. (2018). A TelescopeParam object built using the constructor function TelescopeParam(). This object will trigger qtex() to use the quantification algorithm by Bendall et al. (2019). An atenaParam object built using the constructor function atenaParam(). This object will trigger qtex() to use a quantification algorithm specifically developed in this package.
phenodata	A data.frame or DataFrame object storing phenotypic data to include in the resulting SummarizedExperiment object. If phenodata is set, its row names will become the column names of the resulting SummarizedExperiment object.
mode	One of the pre-defined overlapping methods such as ovUnion(), ovIntersectionStrict or a user-supplied overlapping function. For a user-supplied overlapping function, the input parameters must match those of the pre-defined methods and the function must return a Hits object with subject hits matching the annotated features. This parameter is analogous to the mode parameter of the summarizeOverlaps() function from the GenomicAlignments package.
yieldSize	Field inherited from BamFile. The method for signature ERVmapParam() reads the BAM file by chunks. yieldSize represents the number of records (chunk size) to yield each time the file is read.
verbose	(Default 1). When verbose > 1, detailed information on the quantification steps is provided. Warnings are always present regardless of the value of verbose.
BPPARAM	An object of a BiocParallelParam subclass to configure the parallel execution of the code. By default, a SerialParam object is used, which does not use any parallelization, with the flag progress=TRUE to show progress through the calculations.
auxiliaryFeatures	(Default FALSE). It only applies when 'x' is a ['TelescopeParam'] or an ['atenaParam'] object. When TRUE, auxiliary features created during expression quantification are also returned in the ['SummarizedExperiment'] object.

Details

Giving some AtenaParam object sub-class as input, the qtex() method quantifies the expression of transposable elements (TEs). The particular algorithm to perform the quantification will be selected depending on the specific sub-class of input AtenaParam object, see argument x above.

Value

A SummarizedExperiment object.

References

Jin Y et al. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics. 2015;31(22):3593-3599. DOI: https://doi.org/10.1093/bioinformatics/btv422

Tokuyama M et al. ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses. PNAS, 115(50):12565-12572, 2018. https://doi.org/10.1073/pnas.1814589115

Bendall ML et al. Telescope: characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLOS Computational Biology, 15:e1006453, 2019. https://doi.org/10.1371/journal.pcbi.1006453

See Also

TEtranscriptsParam ERVmapParam TelescopeParam

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,
                   otherLTR=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 Telescope
tspar <- TelescopeParam(bfl=bamfiles,
                        teFeatures=rmskLTR,
                        singleEnd=TRUE,
                        ignoreStrand=TRUE)
## quantify expression
qts <- qtex(tspar)

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