makePWMLognBackground {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.
makePWMLognBackground(bg.seq, motifs, bg.pseudo.count = 1, bg.len = 250, bg.len.sizes = 2^(0:4), bg.source = "", verbose = TRUE, algorithm = "default")
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 |
background sequences will be split into tiles of this length (default: 250bp) |
bg.len.sizes |
background tiles will be joined into bigger tiles containing this much smaller tiles.
The default is |
bg.source |
a free-form textual description of how the background was generated |
verbose |
if to produce verbose output |
algorithm |
type of algorithm to use, valid values are: "default" and "human". |
## 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")) makePWMLognBackground(Dmelanogaster$upstream2000, MotifDb.Dmel.PFM) } ## End(Not run)