motif.find_sites(motif, target,
cutoff = 0.6,
minW = 8,
identities = 0.85,
pvalue = 0.05,
parallel = FALSE,
motif.name = NULL);
motif
the motif PWM model for make the site scan, which could be a SequenceMotif or a MSAMotif object.
target
a fasta sequence collection for make the motif site scan, which can be a single FastaSeq object, a FastaFile object, or a character vector of the raw sequence data.
cutoff#
the minimum similarity score threshold value between the candidate sequence region and the motif PWM model.
minW#
the minimum width of the candidate match site region.
identities
the minimum identity threshold value of the accepted match sites. [as double]
pvalue
the maximum p-value threshold of the accepted match sites. [as double]
parallel
run the site scan task in parallel on multiple cpu cores?. [as boolean]
motif.name
the motif name that will be recorded in the seeds property of the match result. If this parameter is not specified, then the motif name of the given PWM model object will be used. [as string]
env
the R# runtime environment object. [as Environment]
this function returns a R# error message object if the given motif model object or the target sequence data is not a supported data model.