scoreDistEmpirical {motifcounter} | R Documentation |
This function estimates the empirical score distribution on a set of randomly generated DNA sequences based on the background model. This function is only used for benchmarking analysis.
scoreDistEmpirical(pfm, bg, seqlen, nsim)
pfm |
An R matrix that represents a position frequency matrix |
bg |
A Background object |
seqlen |
Integer-valued vector that defines the lengths of the
individual sequences. For a given DNAStringSet,
this information can be retrieved using |
nsim |
Integer number of random samples. |
List containing
Vector of scores
Score distribution
# Load sequences seqfile = system.file("extdata", "seq.fasta", package = "motifcounter") seqs = Biostrings::readDNAStringSet(seqfile) # Load background bg = readBackground(seqs, 1) # Load motif motiffile = system.file("extdata", "x31.tab", package = "motifcounter") motif = t(as.matrix(read.table(motiffile))) # Compoute the empirical score distribution in # sequences of length 1kb using 1000 samples motifcounter:::scoreDistEmpirical(motif, bg, seqlen = 1000, nsim = 1000)