rangeToFastq: rangeToFastq: Extract read information from alignments for...
In wokai/rbamtools: An R package for reading and writing BAM (Binary alignment) files.
Description
Usage
Arguments
Details
Author(s)
Examples
Description
The function rangeToFastq writes all (or selected) aligns
from a bamRange into a compressed fastq file.
Usage
1
rangeToFastq(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 corresponding 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
range2fastq ist deprecated and will be replaced by rangeToFastq soon.
Author(s)
Wolfgang Kaisers
Examples
1
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bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader <- bamReader(bam, idx=TRUE)
coords <- as.integer(c(0, 0, 249250621))
range <- bamRange(reader, coords)
## Not run: rangeToFastq(range, "range.fq.gz")
index <- sample(1:size(range), 100)
## Not run: rangeToFastq(range, "range_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 Author(s) Examples
Description
The function rangeToFastq writes all (or selected) aligns
from a bamRange into a compressed fastq file.
Usage
1 | rangeToFastq(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 corresponding 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
range2fastq ist deprecated and will be replaced by rangeToFastq soon.
Author(s)
Wolfgang Kaisers
Examples
1 2 3 4 5 6 7 | bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader <- bamReader(bam, idx=TRUE)
coords <- as.integer(c(0, 0, 249250621))
range <- bamRange(reader, coords)
## Not run: rangeToFastq(range, "range.fq.gz")
index <- sample(1:size(range), 100)
## Not run: rangeToFastq(range, "range_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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