readerToFastq: readerToFastq: Extraction of a subset of alignments from a...
In wokai/rbamtools: An R package for reading and writing BAM (Binary alignment) files.
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
The function readerToFastq writes (remaining) aligns or
some part of the stored aligns in a BAM file as reads into a
compressed fastq file.
Usage
1
readerToFastq(object, filename, which, append=FALSE)
Arguments
object
bamReader. Must be opened.
filename
Name of output 'fastq' file.
which
(Optional) Logical vector. When given, the routine checks
for each of the given values the value of which. When TRUE the next
retrieved align will be written to the output file,
otherwise will be skipped.
append
(Optional) When TRUE, the routine will append to an
existing file.
Otherwise existing files will be overwritten.
Details
The function 'reader2fastq' is deprecated and will be replaced by
'readerToFastq' soon.
Value
numeric
Author(s)
Wolfgang Kaisers
Examples
1
2
3
4
5
6
7
8
bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader <- bamReader(bam)
## Not run: readerToFastq(reader, "out.fq.gz")
bamClose(reader)
# Reopen in order to point to first align
reader <- bamReader(bam)
index <- sample(1:100, 20)
## Not run: readerToFastq(reader, "out_subset.fq.gz", which=index)
wokai/rbamtools documentation built on May 4, 2019, 9:46 a.m.
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Description Usage Arguments Details Value Author(s) Examples
Description
The function readerToFastq writes (remaining) aligns or
some part of the stored aligns in a BAM file as reads into a
compressed fastq file.
Usage
1 | readerToFastq(object, filename, which, append=FALSE)
|
Arguments
object |
bamReader. Must be opened. |
filename |
Name of output 'fastq' file. |
which |
(Optional) Logical vector. When given, the routine checks for each of the given values the value of which. When TRUE the next retrieved align will be written to the output file, otherwise will be skipped. |
append |
(Optional) When TRUE, the routine will append to an existing file. Otherwise existing files will be overwritten. |
Details
The function 'reader2fastq' is deprecated and will be replaced by 'readerToFastq' soon.
Value
numeric
Author(s)
Wolfgang Kaisers
Examples
1 2 3 4 5 6 7 8 | bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader <- bamReader(bam)
## Not run: readerToFastq(reader, "out.fq.gz")
bamClose(reader)
# Reopen in order to point to first align
reader <- bamReader(bam)
index <- sample(1:100, 20)
## Not run: readerToFastq(reader, "out_subset.fq.gz", which=index)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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