Description Usage Arguments Value Author(s) References See Also Examples
It scans a nucleotide sequence with the pattern represented by a PWMatrix and identifies putative transcription factor binding sites.
1 2 | searchSeq(x, subject, seqname="Unknown", strand="*", min.score="80%",
mc.cores=1L)
|
x |
|
subject |
A |
seqname |
This is sequence name of the target sequence.
If subject is a |
strand |
When searching the sequence, we can search the positive strand or negative strand. While strand is "*", it will search both strands and return the results based on the positvie strand coordinate. |
min.score |
The minimum score for the hit. Can be given an character string in the format of "80%" or as a single absolute value between 0 and 1. When it is percentage value, it represents the quantile between the minimal and the maximal possible value from the PWM. |
mc.cores |
|
A SiteSet
object is returned when x is a PWMatrix
object.
A SiteSetList
object is returned
when x is a PWMatrixList
or subject is a DNAStringSet
.
Ge Tan
Wasserman, W. W., & Sandelin, A. (2004). Applied bioinformatics for the identification of regulatory elements. Nature Publishing Group, 5(4), 276-287. doi:10.1038/nrg1315
searchAln
,
matchPWM
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 | data(MA0003.2)
data(MA0004.1)
pwm1 <- toPWM(MA0003.2)
pwm2 <- toPWM(MA0004.1)
pwmList <- PWMatrixList(pwm1=pwm1, pwm2=pwm2)
seq1 <- "GAATTCTCTCTTGTTGTAGCATTGCCTCAGGGCACACGTGCAAAATG"
seq2 <- "GTTTCACCATTGCCTCAGGGCATAAATATATAAAAAAATATAATTTTCATC"
# PWMatrix, character
## Only scan the positive strand of the input sequence
siteset <- searchSeq(pwm1, seq1, seqname="seq1", strand="+", min.score="80%")
siteset <- searchSeq(pwm1, seq1, seqname="seq1", strand="+", min.score=0.8)
## Only scan the negative strand of the input sequence
siteset <- searchSeq(pwm1, seq1, seqname="seq1", strand="-", min.score="80%")
## Scan both strands of the input sequences
siteset <- searchSeq(pwm1, seq1, seqname="seq1", strand="*", min.score="80%")
## Convert the SiteSet object into other R objects
as(siteset, "data.frame")
as(siteset, "DataFrame")
as(siteset, "GRanges")
writeGFF3(siteset)
writeGFF2(siteset)
# PWMatrixList, character
sitesetList <- searchSeq(pwmList, seq1, seqname="seq1", strand="*",
min.score="80%")
sitesetList <- searchSeq(pwmList, seq1, seqname="seq1", strand="*",
min.score="80%", mc.cores=1L)
## Convert the SiteSteList object into other R objects
as(sitesetList, "data.frame")
as(sitesetList, "DataFrame")
as(sitesetList, "GRanges")
writeGFF3(sitesetList)
writeGFF2(sitesetList)
# PWMatrix, DNAStringSet
library(Biostrings)
seqs <- DNAStringSet(c(seq1=seq1, seq2=seq2))
sitesetList <- searchSeq(pwm1, seqs, min.score="80%")
# PWMatrixList, DNAStringSet
sitesetList <- searchSeq(pwmList, seqs, min.score="80%")
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