countFastaKmers: countFastaKmers function: Counts DNA k-mers from (compressed)...
In wokai/seqTools: Analysis of nucleotide, sequence and quality content on fastq files.
Description
Usage
Arguments
Details
Value
Note
Author(s)
References
Examples
View source: R/fastaFunctions.r
Description
Reads (compressed) fasta files and counts for DNA k-mers in the sequence.
Usage
1
countFastaKmers(filenames,k=4)
Arguments
filenames
character: Vector of fasta file names.
Files can be gz compressed.
k
Length of counted DNA k-mers.
Details
Maximal allowed value for k is 12.
Value
matrix.
Note
The static size of the retured k-mer array is 4^k.
Author(s)
Wolfgang Kaisers
References
Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM
The sanger FASTQ file format for sequences with quality scores and
the Solexa/Illumina FASTQ variants.
Nucleic Acids Research 2010 Vol.38 No.6 1767-177
Examples
1
2
3
4
basedir <- system.file("extdata", package="seqTools")
filename <- file.path(basedir,"small.fa")
## Not run: writeFai(filename, "small.fa.fai")
res <- countFastaKmers(filename, k=2)
wokai/seqTools documentation built on May 4, 2019, 9:46 a.m.
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Description Usage Arguments Details Value Note Author(s) References Examples
View source: R/fastaFunctions.r
Description
Reads (compressed) fasta files and counts for DNA k-mers in the sequence.
Usage
1 | countFastaKmers(filenames,k=4)
|
Arguments
filenames |
|
k |
Length of counted DNA k-mers. |
Details
Maximal allowed value for k is 12.
Value
matrix.
Note
The static size of the retured k-mer array is 4^k.
Author(s)
Wolfgang Kaisers
References
Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM The sanger FASTQ file format for sequences with quality scores and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 2010 Vol.38 No.6 1767-177
Examples
1 2 3 4 | basedir <- system.file("extdata", package="seqTools")
filename <- file.path(basedir,"small.fa")
## Not run: writeFai(filename, "small.fa.fai")
res <- countFastaKmers(filename, k=2)
|
R Package Documentation
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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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