weightedConsensusMatrix: compute weighted consensus matrix
In girafe: Genome Intervals and Read Alignments for Functional Exploration

Description Usage Arguments Value Author(s) See Also Examples

computes weighted consensus matrix

1 2	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

consensusMatrix

 ## 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")