QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
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.
## 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)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
|
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.
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 in x.
width(x):
A vector of non-negative integers containing the number
of letters for each element in x.
nchar(x):
The same as width(x).
names(x):
NULL or a character vector of the same length as x
containing a short user-provided description or comment for each
element in x.
quality(x):
The quality of the strings.
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.
P. Aboyoun
BStringSet, DNAStringSet, RNAStringSet, and AAStringSet objects.
XStringQuality objects.
readDNAStringSet and writeXStringSet
for reading/writing a DNAStringSet object (or other
XStringSet derivative) from/to a FASTA or FASTQ file.
## ---------------------------------------------------------------------
## 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)))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.