Count.SpacedWords: Compute SpacedWords
In crarlus/paprbag: Pathogenicity Prediction of Bacterial Genomes
Description
Usage
Arguments
Value
Author(s)
See Also
View source: R/Count.SpacedWords.R
Description
Count the occurrence of all spaced words
Usage
1
Count.SpacedWords(Reads, k, l, prob = T, symmetric = T)
Arguments
Reads
A DNAStringSet Object
k
The length of the contingous words, i.e. the kmer size
l
The length of the spaced words
prob
If TRUE then the relative frequencies are returned (default TRUE)
symmetric
If TRUE then kmers are returned in their canonical representation (i.e. including their reverse-complement) Default = T
Value
A matrix containing the combined counts for all possible spacer-patterns
Author(s)
Carlus Deneke
See Also
oligonucleotideFrequency
CreateFeaturesFromReads
Other SpacedWordFeatures: Enumerate.SpacerPatterns
crarlus/paprbag documentation built on May 14, 2019, 11:31 a.m.
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Description Usage Arguments Value Author(s) See Also
View source: R/Count.SpacedWords.R
Description
Count the occurrence of all spaced words
Usage
1 | Count.SpacedWords(Reads, k, l, prob = T, symmetric = T)
|
Arguments
Reads |
A DNAStringSet Object |
k |
The length of the contingous words, i.e. the kmer size |
l |
The length of the spaced words |
prob |
If TRUE then the relative frequencies are returned (default TRUE) |
symmetric |
If TRUE then kmers are returned in their canonical representation (i.e. including their reverse-complement) Default = T |
Value
A matrix containing the combined counts for all possible spacer-patterns
Author(s)
Carlus Deneke
See Also
oligonucleotideFrequency
CreateFeaturesFromReads
Other SpacedWordFeatures: Enumerate.SpacerPatterns
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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