kMerIndex: kMerIndex function: Returns array index for given DNA k-mers.

In seqTools: Analysis of nucleotide, sequence and quality content on fastq files.

Description

For each k, there exist $4^k$ DNA k-mers. Many functions inside this package return values where DNA k-mers appear as array indices. kMerIndex can be used for extraction of count values for special k-mers by provision of index values.

Usage

kMerIndex(kMers, k=nchar(kMers)[1], base = 1)

Arguments

kMers	character. Vector of equal sized character strings. The number of characters in each string must be =k (i.e. all(nchar(kMers)==k))
k	integer. Length of k-mer.
base	integer. Value must be 0 or 1 (i.e. length(base)==1). For base=0 the returned index is 0-based (i.e. the index of the first k-mer (AAA..)) is 0. Otherwise the index is 1-based.

Details

Maximal allowed value for k is 12.

Value

integer.

Author(s)

Wolfgang Kaisers

Examples

kMerIndex(c("AACC","ATAA"))
kMerIndex(c("AA","AC"),base=1)
kMerIndex(c("AA","AC"),base=0)

seqTools documentation built on May 2, 2019, 4:45 p.m.