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aaiezza/nucleotidesSlidingWindow.R

Created July 14, 2017 18:13
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Nucleotides Sliding Window
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nucleotidesSlidingWindow.R
require( zoo )
require( iterpc )
# Could be retreived from anywhere of course…
nucleotideSequence <- sample( c('A','T','C','G'), 1000, replace=TRUE, prob=c(.1,.1,.4,.4) )
windowWidth <- 3
kmers <- rollapply( nucleotideSequence, width = windowWidth, by = 1, paste, collapse='' )
possibleKmers <- apply( getall( iterpc(4, 3, c('A','T','C','G'), replace = TRUE) ), 1, paste, collapse = '' )
table( factor( kmers, levels = possibleKmers ) )
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