TelescopeParam-class {atena} | R Documentation |
This is a class for storing parameters provided to the Telescope algorithm.
Build an object of the class TelescopeParam
.
TelescopeParam( bfl, teFeatures, aggregateby = character(0), geneFeatures = NA, singleEnd = TRUE, strandMode = 1L, ignoreStrand = FALSE, fragments = FALSE, pi_prior = 0L, theta_prior = 0L, em_epsilon = 1e-07, maxIter = 100L ) ## S4 method for signature 'TelescopeParam' show(object)
bfl |
A |
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
( |
strandMode |
(Default 1) Numeric vector which can take values 0, 1 or
2.
The strand mode is a per-object switch on
|
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 |
fragments |
(Default TRUE) A logical; applied to paired-end data only.
When |
pi_prior |
(Default 0) A positive integer scalar indicating the prior on pi. This is equivalent to adding n unique reads. |
theta_prior |
(Default 0) A positive integer scalar storing the prior on Q. Equivalent to adding n non-unique reads. |
em_epsilon |
(Default 1e-7) A numeric scalar indicating the EM Algorithm Epsilon cutoff. |
maxIter |
A positive integer scalar storing the maximum number of
iterations of the EM SQUAREM algorithm (Du and Varadhan, 2020). Default
is 100 and this value is passed to the |
object |
A TelescopeParam object. |
This is the constructor function for objects of the class
TelescopeParam-class
. This type of object is the input to the
function qtex()
for quantifying expression of transposable
elements, which will call the Telescope algorithm
Bendall et al. (2019)
with this type of object.
A TelescopeParam object.
singleEnd
(Default TRUE) Logical value indicating if reads are single
(TRUE
) or paired-end (FALSE
).
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 strandMode
is ignored.
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
is considered to be overlapping an annotated feature as long as they
have a non-empty intersecting genomic range on the same strand, while when
ignoreStrand = TRUE
the strand is not considered.
fragments
(Default FALSE) A logical; applied to paired-end data only.
When fragments=FALSE
(default), the read-counting method only counts
‘mated pairs’ from opposite strands, while when fragments=TRUE
,
same-strand pairs, singletons, reads with unmapped pairs and other fragments
are also counted. For further details see
summarizeOverlaps()
.
pi_prior
(Default 0) A positive integer scalar indicating the prior on pi. This is equivalent to adding n unique reads.
theta_prior
(Default 0) A positive integer scalar storing the prior on Q. Equivalent to adding n non-unique reads.
em_epsilon
(Default 1e-7) A numeric scalar indicating the EM Algorithm Epsilon cutoff.
maxIter
A positive integer scalar storing the maximum number of
iterations of the EM SQUAREM algorithm (Du and Varadhan, 2020). Default
is 100 and this value is passed to the maxiter
parameter of the
squarem()
function.
Bendall et al. Telescope: characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLOS Comp. Biol. 2019;15(9):e1006453. DOI: https://doi.org/10.1371/journal.pcbi.1006453
Bendall et al. Telescope: characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLOS Comp. Biol. 2019;15(9):e1006453. DOI: https://doi.org/10.1371/journal.pcbi.1006453
bamfiles <- list.files(system.file("extdata", package="atena"), pattern="*.bam", full.names=TRUE) TE_annot <- readRDS(file = system.file("extdata", "Top28TEs.rds", package="atena")) gene_annot <- readRDS(file = system.file("extdata", "Top50genes.rds", package="atena")) tspar <- TelescopeParam(bfl=bamfiles, teFeatures=TE_annot, geneFeatures = gene_annot, singleEnd = TRUE, ignoreStrand=TRUE) tspar