QualityScaledXStringSet-class {Biostrings} | R Documentation |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
Description
The QualityScaledBStringSet class is a container for storing a
BStringSet
object with an XStringQuality
object.
Similarly, the QualityScaledDNAStringSet (or QualityScaledRNAStringSet, or
QualityScaledAAStringSet) class is a container for storing a
DNAStringSet
(or RNAStringSet
, or
AAStringSet
) objects with an XStringQuality
object.
Usage
## Constructors:
QualityScaledBStringSet(x, quality)
QualityScaledDNAStringSet(x, quality)
QualityScaledRNAStringSet(x, quality)
QualityScaledAAStringSet(x, quality)
## Read/write a QualityScaledXStringSet object from/to a FASTQ file:
readQualityScaledDNAStringSet(filepath,
quality.scoring=c("phred", "solexa", "illumina"),
nrec=-1L, skip=0L, seek.first.rec=FALSE,
use.names=TRUE)
writeQualityScaledXStringSet(x, filepath, append=FALSE,
compress=FALSE, compression_level=NA)
Arguments
x |
For the For |
quality |
An XStringQuality derivative. |
filepath , nrec , skip , seek.first.rec , use.names , append , compress , compression_level |
See |
quality.scoring |
Specify the quality scoring used in the FASTQ file. Must be one of
|
Details
The QualityScaledBStringSet
, QualityScaledDNAStringSet
,
QualityScaledRNAStringSet
and QualityScaledAAStringSet
functions are constructors that can be used to "naturally" turn
x
into an QualityScaledXStringSet object of the desired base type.
Accessor methods
The QualityScaledXStringSet class derives from the XStringSet
class hence all the accessor methods defined for an XStringSet
object can also be used on an QualityScaledXStringSet object. Common
methods include (in the code snippets below, x
is an
QualityScaledXStringSet object):
-
length(x)
: The number of sequences inx
. -
width(x)
: A vector of non-negative integers containing the number of letters for each element inx
. -
nchar(x)
: The same aswidth(x)
. -
names(x)
:NULL
or a character vector of the same length asx
containing a short user-provided description or comment for each element inx
. -
quality(x)
: The quality of the strings.
Subsetting and appending
In the code snippets below,
x
and values
are XStringSet objects,
and i
should be an index specifying the elements to extract.
-
x[i]
: Return a new QualityScaledXStringSet object made of the selected elements.
Author(s)
P. Aboyoun
See Also
-
BStringSet, DNAStringSet, RNAStringSet, and AAStringSet objects.
-
XStringQuality objects.
-
readDNAStringSet
andwriteXStringSet
for reading/writing a DNAStringSet object (or other XStringSet derivative) from/to a FASTA or FASTQ file.
Examples
## ---------------------------------------------------------------------
## QualityScaled*StringSet() CONSTRUCTORS
## ---------------------------------------------------------------------
x1 <- DNAStringSet(c("TTGA", "CTCN"))
q1 <- PhredQuality(c("*+,-", "6789"))
qdna1 <- QualityScaledDNAStringSet(x1, q1)
qdna1
## ---------------------------------------------------------------------
## READ/WRITE A QualityScaledDNAStringSet OBJECT FROM/TO A FASTQ FILE
## ---------------------------------------------------------------------
filepath <- system.file("extdata", "s_1_sequence.txt",
package="Biostrings")
## By default, readQualityScaledDNAStringSet() assumes that the FASTQ
## file contains "Phred quality scores" (this is the standard Sanger
## variant to assess reliability of a base call):
qdna2 <- readQualityScaledDNAStringSet(filepath)
qdna2
outfile2a <- tempfile()
writeQualityScaledXStringSet(qdna2, outfile2a)
outfile2b <- tempfile()
writeQualityScaledXStringSet(qdna2, outfile2b, compress=TRUE)
## Use 'quality.scoring="solexa"' or 'quality.scoring="illumina"' if the
## quality scores are Solexa quality scores:
qdna3 <- readQualityScaledDNAStringSet(filepath, quality.scoring="solexa")
qdna3
outfile3a <- tempfile()
writeQualityScaledXStringSet(qdna3, outfile3a)
outfile3b <- tempfile()
writeQualityScaledXStringSet(qdna3, outfile3b, compress=TRUE)
## Sanity checks:
stopifnot(identical(readLines(outfile2a), readLines(filepath)))
stopifnot(identical(readLines(outfile2a), readLines(outfile2b)))
stopifnot(identical(readLines(outfile3a), readLines(filepath)))
stopifnot(identical(readLines(outfile3a), readLines(outfile3b)))