R: Read aligned reads and their quality scores into R representations

readAligned {ShortRead}

R Documentation

Read aligned reads and their quality scores into R representations

Description

readAligned reads all aligned read files in a directory dirPath whose file name matches pattern, returning a compact internal representation of the alignments, sequences, and quality scores in the files. Methods read all files into a single R object; a typical use is to restrict input to a single aligned read file.

Usage


readAligned(dirPath, pattern=character(0), ...)

Arguments

`dirPath`	A character vector (or other object; see methods defined on this generic) giving the directory path (relative or absolute) of aligned read files to be input.
`pattern`	The (`grep`-style) pattern describing file names to be read. The default (`character(0)`) results in (attempted) input of all files in the directory.
`...`	Additional arguments, used by methods. Most methods implement `filter=srFilter()`, allowing objects of `SRFilter` to selectively returns aligned reads.

Details

There is no standard aligned read file format; methods parse particular file types.

The readAligned,character-method interprets file types based on an additional type argument. Supported types are:

type="SolexaExport"

This type parses .*_export.txt files following the documentation in the Solexa Genome Alignment software manual, version 0.3.0. These files consist of the following columns; consult Solexa documentation for precise descriptions. If parsed, values can be retrieved from AlignedRead as follows:

Machine: Ignored
Run number: stored in alignData
Lane: stored in alignData
Tile: stored in alignData
X: stored in alignData
Y: stored in alignData
Index string: Ignored
Read number: Ignored
Read: sread
Quality: quality
Match chromosome: chromosome
Match contig: Ignored
Match position: position
Match strand: strand
Match description: Ignored
Single-read alignment score: alignQuality
Paired-read alignment score: Ignored
Partner chromosome: Ignored
Partner contig: Ignored
Partner offset: Ignored
Partner strand: Ignored
Filtering: alignData

Paired read columns are not interpreted. The resulting AlignedRead object does not contain a meaningful id; instead, use information from alignData to identify reads.

Different interfaces to reading alignment files are described in SolexaPath and SolexaSet.

type="SolexaPrealign"

See SolexaRealign

type="SolexaAlign"

See SolexaRealign

type="SolexaRealign"

These types parse s_L_TTTT_prealign.txt, s_L_TTTT_align.txt or s_L_TTTT_realign.txt files produced by default and eland analyses. From the Solexa documentation, align corresponds to unfiltered first-pass alignements, prealign adjusts alignments for error rates (when available), realign filters alignments to exclude clusters failing to pass quality criteria.

Because base quality scores are not stored with alignments, the object returned by readAligned scores all base qualities as -32.

If parsed, values can be retrieved from AlignedRead as follows:

Sequence: stored in sread
Best score: stored in alignQuality
Number of hits: stored in alignData
Target position: stored in position
Strand: stored in strand
Target sequence: Ignored; parse using readXStringColumns
Next best score: stored in alignData

type="MAQMap", records=-1L

Parse binary map files produced by MAQ. See details in the next section. The records option determines how many lines are read; -1L (the default) means that all records are input.

type="MAQMapShort", records=-1L

The same as type="MAQMap" but for map files made with Maq prior to version 0.7.0. (These files use a different maximum read length [64 instead of 128], and are hence incompatible with newer Maq map files.)

type="MAQMapview"

Parse alignment files created by MAQ's ‘mapiew’ command. Interpretation of columns is based on the description in the MAQ manual, specifically


        ...each line consists of read name, chromosome, position,
        strand, insert size from the outer coordinates of a pair,
        paired flag, mapping quality, single-end mapping quality,
        alternative mapping quality, number of mismatches of the
        best hit, sum of qualities of mismatched bases of the best
        hit, number of 0-mismatch hits of the first 24bp, number
        of 1-mismatch hits of the first 24bp on the reference,
        length of the read, read sequence and its quality.

The read name, read sequence, and quality are read as XStringSet objects. Chromosome and strand are read as factors. Position is numeric, while mapping quality is numeric. These fields are mapped to their corresponding representation in AlignedRead objects.

Number of mismatches of the best hit, sum of qualities of mismatched bases of the best hit, number of 0-mismatch hits of the first 24bp, number of 1-mismatch hits of the first 24bp are represented in the AlignedRead object as components of alignData.

Remaining fields are currently ignored.

Value

A single R object (e.g., AlignedRead) containing alignments, sequences and qualities of all files in dirPath matching pattern. There is no guarantee of order in which files are read.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>, Simon Anders <anders@ebi.ac.uk> (MAQ map)

Examples

sp <- SolexaPath(system.file("extdata", package="ShortRead"))
ap <- analysisPath(sp)
## ELAND_EXTENDED
readAligned(ap, "s_2_export.txt", "SolexaExport")
## PhageAlign
readAligned(ap, "s_5_.*_realign.txt", "SolexaRealign")

## MAQ
dirPath <- system.file('extdata', 'maq', package='ShortRead')
list.files(dirPath)
## First line
readLines(list.files(dirPath, full.names=TRUE)[[1]], 1)
countLines(dirPath)
## two files collapse into one
readAligned(dirPath, type="MAQMapview")

## select only chr1-5.fa, '+' strand
filt <- compose(chromosomeFilter("chr[1-5].fa"),
                strandFilter("+"))
readAligned(sp, "s_2_export.txt", filter=filt)

[Package ShortRead version 1.0.7 Index]