ERVmapParam-class {atena} | R Documentation |
This is a class for storing parameters provided to the ERVmap algorithm. It is a subclass of the 'AtenaParam-class'.
Build an object of the class ERVmapParam
ERVmapParam( bfl, teFeatures, aggregateby = character(0), geneFeatures = NA, singleEnd = TRUE, ignoreStrand = TRUE, strandMode = 1L, fragments = !singleEnd, maxMismatchRate = 0.02, suboptimalAlignmentTag = "auto", suboptimalAlignmentCutoff = 5, geneCountMode = "all" ) ## S4 method for signature 'ERVmapParam' show(object)
bfl |
A |
teFeatures |
A |
aggregateby |
Character vector with column names in 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 TRUE) 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 not |
maxMismatchRate |
(Default 0.02) Numeric value storing the maximum mismatch rate employed by the ERVmap algorithm to discard aligned reads whose rate of sum of hard and soft clipping or whose rate of the edit distance over the genome reference to the length of the read is above this threshold. |
suboptimalAlignmentTag |
(Default "auto") Character string storing the
tag name in the BAM files that stores the suboptimal alignment score used in
the third filter of ERVmap; see
Tokuyama et al. (2018).
The default, |
suboptimalAlignmentCutoff |
(Default 5) Numeric value storing the
cutoff above which the difference between the alignment score and the
suboptimal alignment score is considered sufficiently large to retain the
alignment. When this value is set to |
geneCountMode |
(Default |
object |
A ERVmapParam object. |
This is the constructor function for objects of the class
ERVmapParam-class
. This type of object is the input to the
function qtex()
for quantifying expression of transposable
elements using the ERVmap method
Tokuyama et al. (2018). The
ERVmap algorithm processes reads following conservative filtering criteria
to provide reliable raw count data for each TE.
A ERVmapParam object.
readMapper
The name of the software used to align reads, obtained from the BAM file header.
singleEnd
(Default FALSE) 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 TRUE) A logical which defines if the strand
should be taken into consideration when computing the overlap between reads
and TEs in the annotations. When ignore_strand = FALSE
, only those
reads which overlap the TE and are on the same strand are counted. On the
contrary, when ignore_strand = TRUE
, any read overlapping an element
in teFeatures
is counted regardless of the strand.
fragments
(Default not singleEnd
) A logical; applied to
paired-end data only. When fragments=TRUE
(default), the
read-counting method in the original ERVmap algorithm will be applied: each
mate of a paired-end read is counted once and, therefore, two mates mapping
to the same element result in adding up a count value of two. When
fragments=FALSE
, if the two mates of a paired-end read map to the
same element, they are counted as a single hit and singletons, reads with
unmapped pairs and other fragments, are not counted.
maxMismatchRate
(Default 0.02) Numeric value storing the maximum mismatch rate employed by the ERVmap algorithm to discard aligned reads whose rate of sum of hard and soft clipping, or of the edit distance over the genome reference, to the length of the read is above this threshold.
suboptimalAlignmentTag
(Default "auto") Character string storing the
tag name in the BAM files that stores the suboptimal alignment score used in
the third filter of ERVmap; see Tokuyama et al. (2018). The default,
suboptimalAlignmentTag="auto"
, assumes that either the BAM files were
generated by BWA and include a tag called XS
that stores the
suboptimal alignment score or, if the XS
tag is not available, then
it uses the available secondary alignments to implement an analogous
approach to that of the third ERVmap filter. When
suboptimalAlignmentTag="none"
, it also performs the latter approach
even when the tag XS
is available.
When this parameter is different from "auto"
and "none"
, a tag
with the given name is used to extract the suboptimal alignment score.
The absence of that tag will prompt an error.
suboptimalAlignmentCutoff
(Default 5) Numeric value storing the cutoff
above which the difference between the alignment score and the suboptimal
alignment score is considered sufficiently large to retain the alignment.
When this value is set to NA
, then the filtering step based on
suboptimal alignment scores is skipped.
geneCountMode
(Default "all") Character string indicating if the ERVmap read filters applied to quantify TEs expression should also be applied when quantifying gene expression ("ervmap") or not ("all"), in which case all primary alignments mapping to genes are counted.
Tokuyama M et al. ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses. PNAS. 2018;115(50):12565-12572. DOI: https://doi.org/10.1073/pnas.1814589115
Tokuyama M et al. ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses. PNAS. 2018;115(50):12565-12572. DOI: https://doi.org/10.1073/pnas.1814589115
bamfiles <- list.files(system.file("extdata", package="atena"), pattern="*.bam", full.names=TRUE) TE_annot <- readRDS(file = system.file("extdata", "Top28TEs.rds", package="atena")) empar <- ERVmapParam(bamfiles, teFeatures = TE_annot, singleEnd = TRUE, ignoreStrand = TRUE, suboptimalAlignmentCutoff=NA) empar