weightedConsensusMatrix {girafe} | R Documentation |
computes weighted consensus matrix
weightedConsensusMatrix(seqs, weights, shift = NULL, baseLetters = c("A", "C", "G", "T", "N"))
seqs |
character vector of read sequences |
weights |
integer; weights (read counts) |
shift |
integer; shift of each read sequence relative to the first column of the consensus matrix, by default: 0 |
baseLetters |
alphabet |
A consensus matrix
J Toedling
## Align following sequences with weights: ## ACATT 1 ## CGTTA 10 ## TTG 3 ## GACATT 4 dweights <- c(1L, 10L, 3L, 4L) d <- c("ACATT","CGTTA", "TTG", "GACATT") dshifts <- c(0L, 1L, 2L, -1L) W <- girafe:::weightedConsensusMatrix(d, dweights, shift=dshifts) consensusString(W, ambiguityMap="N")