kmer_by_gene: Count Kmers within each sequence of a DNAStringSet
In TaliaferroLab/FeatureReachR: Extract Enriched Biological Features From RNA-seq Data
Description
Usage
Arguments
Value
See Also
Examples
Description
This function simply returns the counts of each kmer for each gene in a
DNAStringSet.
Usage
1
kmer_by_gene(DNAStringSet, k)
Arguments
DNAStringSet
A DNAStringSet Object. Use
readDNAStringSet on a fasta file to create.
k
An Integer. The length of kmers to count. Values 3 < k < 8 are
recommended.
Value
a dataframe containing kmer counts across each sequences within the DNAStringSet
See Also
write_Sequence, readDNAStringSet,
oligonucleotideFrequency, kmer_compare
Examples
1
2
case_fasta <- Biostrings::readDNAStringSet("example_case.fa")
case_fasta_kmer_counts <- kmer_by_gene(case_fasta, 6)
TaliaferroLab/FeatureReachR documentation built on Aug. 15, 2021, 2:21 p.m.
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Description Usage Arguments Value See Also Examples
Description
This function simply returns the counts of each kmer for each gene in a DNAStringSet.
Usage
1 | kmer_by_gene(DNAStringSet, k)
|
Arguments
DNAStringSet |
A DNAStringSet Object. Use
|
k |
An Integer. The length of kmers to count. Values 3 < k < 8 are recommended. |
Value
a dataframe containing kmer counts across each sequences within the DNAStringSet
See Also
write_Sequence, readDNAStringSet,
oligonucleotideFrequency, kmer_compare
Examples
1 2 | case_fasta <- Biostrings::readDNAStringSet("example_case.fa")
case_fasta_kmer_counts <- kmer_by_gene(case_fasta, 6)
|
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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