AlignedRead-class: (Legacy) "AlignedRead" class for aligned short reads
In ShortRead: FASTQ input and manipulation

Description Objects from the Class Slots Extends Methods Author(s) See Also Examples

This class represents and manipulates reads and their genomic alignments. Alignment information includes genomic position, strand, quality, and other data.

Objects of this class can be created from a call to the AlignedRead constructor, or more typically by parsing appropriate files (e.g., readAligned).

chromosome: Object of class "factor" the particular sequence within a set of target sequences (e.g. chromosomes in a genome assembly) to which each short read aligns.
position: Object of class "integer" the (base-pair) position in the genome to which the read is aligned. AlignedRead objects created by readAligned use 1-based indexing, with alignemnts reported in ‘left-most’ coordinates, as described in the vignette.
strand: Object of class "factor" the strand of the alignment.
alignQuality: Object of class "numeric" representing an alignment quality score.
alignData: Object of class "AlignedDataFrame" additional alignment information.
quality: Object of class "BStringSet" representing base-call read quality scores.
sread: Object of class "DNAStringSet" DNA sequence of the read.
id: Object of class "BStringSet" read identifier.

Class "ShortReadQ", directly. Class "ShortRead", by class "ShortReadQ", distance 2. Class ".ShortReadBase", by class "ShortReadQ", distance 3.

See accessors for additional functions to access slot content, and ShortReadQ, ShortRead for inherited methods. Additional methods include:

[

signature(x = "AlignedRead", i = "ANY", j = "missing"): This method creates a new AlignedRead object containing only those reads indexed by i. chromosome is recoded to contain only those levels in the new subset.

append

signature(x = "AlignedRead", values = "AlignedRead"): append values after x. chromosome and strand must be factors with the same levels. See methods for ShortReadQ, AlignedDataFrame for details of how these components of x and y are appended.

coerce

signature(from = "PairwiseAlignments", to = "AlignedRead"):

signature(from = "AlignedRead", to = "IntegerRangesList"): signature(from = "AlignedRead", to = "GRanges"): signature(from = "AlignedRead", to = "GAlignments"): signature(from = "AlignedRead", to = "GappedReads"):

Invoke these methods with, e.g., as(from, "AlignedRead") to coerce objects of class from to class "AlignedRead".

Coercion from AlignedRead to IntegerRangesList or GRanges assumes that position(from) uses a ‘leftmost’ (see coverage on this page) coordinate system. Since IntegerRangesList objects cannot store NA values, reads with NA in the position, width, chromosome or (in the case of GRanges) strand vectors are dropped.

chromosome

signature(object = "AlignedRead"): access the chromosome slot of object.

position

signature(object = "AlignedRead"): access the position slot of object.

strand

signature(object = "AlignedRead"): access the strand slot of object.

coverage

signature(x = "AlignedRead", shift = 0L, width = NULL, weight = 1L, ..., coords = c("leftmost", "fiveprime"), extend=0L):

Calculate coverage across reads present in x.

shift must be either 0L or a named integer vector with names including all levels(chromosome(x)). It specifies how the reads in x should be (horizontally) shifted before the coverage is computed.

width must be either NULL or a named vector of non-negative integers with names including all levels(chromosome(x)). In the latter case, it specifies for each chromosome the end of the chromosome region over which coverage is to be calculated after the reads have been shifted. Note that this region always starts at chromosome position 1. If width is NULL, it ends at the rightmost chromosome position covered by at least one read.

weight must be 1L for now (weighting the reads is not supported yet, sorry).

coords specifies the coordinate system used to record position. Both systems number base pairs from left to right on the 5' strand. leftmost indicates the eland convention, where position(x) is the left-most (minimum) base pair, regardless of strand. fiveprime is the MAQ convention, where position(x) is the coordinate of the 5' end of the aligned read.

extend indicates the number of base pairs to extend the read. Extension is in the 3' direction, measured from the 3' end of the aligned read.

The return value of coverage is a SimpleRleList object.

%in%

signature(x = "AlignedRead", table = "IntegerRangesList"):

Return a length(x) logical vector indicating whether the chromosome, position, and width of x overlap with ranges in table. Reads for which chromosome(), position(), or width() return NA never overlap with table. This function assumes that positions are in ‘leftmost’ coordinates, as defined in coverage.

srorder

signature(x = "AlignedRead", ..., withSread=TRUE):

srrank

signature(x = "AlignedRead", ..., withSread=TRUE):

srsort

signature(x = "AlignedRead", ..., withSread=TRUE):

srduplicated

signature(x = "AlignedRead", ..., withSread=TRUE):

Order, rank, sort, and find duplicates in AlignedRead objects. Reads are sorted by chromosome, strand, position, and then (if withSread=TRUE) sread; less fine-grained sorting can be accomplished with, e.g., x[srorder(sread(x))]. srduplicated behaves like duplicated, i.e., the first copy of a duplicate is FALSE while the remaining copies are TRUE.

show

signature(object = "AlignedRead"): provide a compact display of the AlignedRead content.

detail

signature(x = "AlignedRead"): display alignData in more detail.

Martin Morgan <mtmorgan@fhcrc.org>

readAligned

showMethods(class="AlignedRead", where=getNamespace("ShortRead"))
dirPath <- system.file('extdata', 'maq', package='ShortRead')
(aln <- readAligned(dirPath, 'out.aln.1.txt', type="MAQMapview"))
coverage(aln)[[1]]
cvg <- coverage(aln, shift=c(ChrA=10L))
## remove 0 coverage on left ends
ltrim0 <- function(x) {
    i <- !cumprod(runValue(x) == 0)
    Rle(runValue(x)[i], runLength(x)[i])
}
endoapply(cvg, ltrim0)
## demonstration of show() and detail() methods
show(aln)
detail(aln)