Description Usage Arguments Value Author(s) See Also Examples
Utilities for BSgenome objects.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24  ## S4 method for signature 'BSgenome'
matchPWM(pwm, subject, min.score = "80%", exclude = "",
maskList = logical(0))
## S4 method for signature 'BSgenome'
countPWM(pwm, subject, min.score = "80%", exclude = "",
maskList = logical(0))
## S4 method for signature 'BSgenome'
vmatchPattern(pattern, subject, max.mismatch = 0, min.mismatch = 0,
with.indels = FALSE, fixed = TRUE, algorithm = "auto",
exclude = "", maskList = logical(0), userMask =
IRangesList(), invertUserMask = FALSE)
## S4 method for signature 'BSgenome'
vcountPattern(pattern, subject, max.mismatch = 0, min.mismatch = 0,
with.indels = FALSE, fixed = TRUE, algorithm = "auto",
exclude = "", maskList = logical(0), userMask =
IRangesList(), invertUserMask = FALSE)
## S4 method for signature 'BSgenome'
vmatchPDict(pdict, subject, max.mismatch = 0, min.mismatch = 0,
fixed = TRUE, algorithm = "auto", verbose = FALSE,
exclude = "", maskList = logical(0))
## S4 method for signature 'BSgenome'
vcountPDict(pdict, subject, max.mismatch = 0, min.mismatch = 0,
fixed = TRUE, algorithm = "auto", collapse = FALSE,
weight = 1L, verbose = FALSE, exclude = "", maskList = logical(0))

pwm 
A numeric matrix with row names A, C, G and T representing a Position Weight Matrix. 
pattern 
A DNAString object containing the pattern sequence. 
pdict 
A DNAStringSet object containing the pattern sequences. 
subject 
A BSgenome object containing the subject sequences. 
min.score 
The minimum score for counting a match.
Can be given as a character string containing a percentage (e.g.

max.mismatch, min.mismatch 
The maximum and minimum number of mismatching letters allowed (see

with.indels 
If 
fixed 
If 
algorithm 
For For 
collapse, weight 
ignored arguments. 
verbose 

exclude 
A character vector with strings that will be used to filter out chromosomes whose names match these strings. 
maskList 
A named logical vector of maskStates preferred when used with a BSGenome object. When using the bsapply function, the masks will be set to the states in this vector. 
userMask 
An IntegerRangesList, containing a mask to be applied
to each chromosome. See 
invertUserMask 
Whether the 
A GRanges object for matchPWM
with two
elementMetadata columns: "score" (numeric), and "string" (DNAStringSet).
A GRanges object for vmatchPattern
.
A GRanges object for vmatchPDict
with
one elementMetadata column: "index", which represents a mapping to a
position in the original pattern dictionary.
A data.frame object for countPWM
and vcountPattern
with three columns: "seqname" (factor), "strand" (factor), and
"count" (integer).
A DataFrame object for vcountPDict
with four
columns: "seqname" ('factor' Rle), "strand" ('factor' Rle),
"index" (integer) and "count" ('integer' Rle). As with vmatchPDict
the index column represents a mapping to a position in the original
pattern dictionary.
P. Aboyoun
matchPWM
,
matchPattern
,
matchPDict
,
bsapply
1 2 3 4 5 6 7 8 9 10 11 12 13  library(BSgenome.Celegans.UCSC.ce2)
data(HNF4alpha)
pwm < PWM(HNF4alpha)
matchPWM(pwm, Celegans)
countPWM(pwm, Celegans)
pattern < consensusString(HNF4alpha)
vmatchPattern(pattern, Celegans, fixed = "subject")
vcountPattern(pattern, Celegans, fixed = "subject")
vmatchPDict(HNF4alpha[1:10], Celegans)
vcountPDict(HNF4alpha[1:10], Celegans)

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