makePWMGEVBackground {PWMEnrich} | R Documentation |
Construct a lognormal background distribution for a set of sequences. Sequences concatenated are binned in 'bg.len' chunks and lognormal distribution fitted to them.
makePWMGEVBackground(bg.seq, motifs, bg.pseudo.count = 1, bg.len = seq(200, 2000, 200), bg.source = "", verbose = TRUE, fit.log = TRUE)
bg.seq |
a set of background sequences, either a list of DNAString object or DNAStringSet object |
motifs |
a set of motifs, either a list of frequency matrices, or a list of PWM objects. If frequency matrices are given, the background distribution is fitted from bg.seq. |
bg.pseudo.count |
the pseudo count which is shared between nucleotides when frequency matrices are given |
bg.len |
the length range of background chunks |
bg.source |
a free-form textual description of how the background was generated |
verbose |
if to produce verbose output |
fit.log |
if to fit log odds (instead of odds) |
## Not run: if(require("PWMEnrich.Dmelanogaster.background")){ data(MotifDb.Dmel.PFM) # make background for MotifDb motifs using 2kb promoters of all D. melanogaster transcripts if(require("BSgenome.Dmelanogaster.UCSC.dm3")) makePWMGEVBackground(Dmelanogaster$upstream2000, MotifDb.Dmel.PFM) } ## End(Not run)