TEtranscriptsParam-class {atena} | R Documentation |
This is a class for storing parameters provided to the TEtranscripts algorithm. It is a subclass of the 'AtenaParam-class'.
Build an object of the class TEtranscriptsParam
TEtranscriptsParam( bfl, teFeatures, aggregateby = character(0), geneFeatures = NA, singleEnd = TRUE, ignoreStrand = FALSE, strandMode = 1L, fragments = TRUE, tolerance = 1e-04, maxIter = 100L ) ## S4 method for signature 'TEtranscriptsParam' show(object)
bfl |
a character string vector of BAM file names. |
teFeatures |
A |
aggregateby |
Character vector with column names from the annotation
to be used to aggregate quantifications. By default, this is an empty
vector, which means that the names of the input |
geneFeatures |
A |
singleEnd |
(Default TRUE) Logical value indicating if reads are single
( |
ignoreStrand |
(Default FALSE) A logical which defines if the strand
should be taken into consideration when computing the overlap between reads
and annotated features. When |
strandMode |
(Default 1) Numeric vector which can take values 0, 1 or
2.
The strand mode is a per-object switch on
|
fragments |
(Default TRUE) A logical; applied to paired-end data only.
When |
tolerance |
A positive numeric scalar storing the minimum tolerance
above which the SQUAREM algorithm (Du and Varadhan, 2020) keeps iterating.
Default is |
maxIter |
A positive integer scalar storing the maximum number of
iterations of the SQUAREM algorithm (Du and Varadhan, 2020). Default
is 100 and this value is passed to the |
object |
A TEtranscriptsParam object. |
This is the constructor function for objects of the class
TEtranscriptsParam-class
. This type of object is the input to the
function qtex()
for quantifying expression of transposable
elements using the TEtranscripts method
Jin et al. (2015). The
TEtranscripts algorithm quantifies TE expression by using an EM algorithm
to optimally distribute ambiguously mapped reads.
A TEtranscriptsParam object.
singleEnd
(Default FALSE) Logical value indicating if reads are single
(TRUE
) or paired-end (FALSE
).
ignoreStrand
(Default FALSE) A logical which defines if the strand
should be taken into consideration when computing the overlap between reads
and annotated features. When ignoreStrand = FALSE
, an aligned read
will be considered to be overlapping an annotated feature as long as they
have a non-empty intersecting genomic ranges on the same strand, while when
ignoreStrand = TRUE
the strand will not be considered.
strandMode
(Default 1) Numeric vector which can take values 0, 1 or 2.
The strand mode is a per-object switch on
GAlignmentPairs
objects that controls the behavior of the strand getter. See
GAlignmentPairs
class for further detail. If singleEnd = TRUE
, then use either
strandMode = NULL
or do not specify the strandMode
parameter.
fragments
(Default TRUE) A logical; applied to paired-end data only.
When fragments=TRUE
(default), the read-counting method will also
count reads without mates, while when fragments=FALSE
those reads
will not be counted. For further details see
summarizeOverlaps()
.
tolerance
A positive numeric scalar storing the minimum tolerance
above which the SQUAREM algorithm (Du and Varadhan, 2020) keeps iterating.
Default is 1e-4
and this value is passed to the tol
parameter
of the squarem()
function.
maxIter
A positive integer scalar storing the maximum number of
iterations of the SQUAREM algorithm (Du and Varadhan, 2020). Default
is 100 and this value is passed to the maxiter
parameter of the
squarem()
function.
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
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
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")) ttpar