Description Value Methods Author(s) Examples
Get the genomic coordinates from SitePairSetList.
A list of two GRanges
objects are returned,
one for the target sequences
and another for query sequences.
In the GRanges
, strand is taken from the Axt
object.
In the meta-data columns, PWM matrix ID, the strand of matrix and
match score are also returned.
signature(x = "SitePairSetList", axt = "Axt")
Convert the relative coordinates to absolute coordinates.
Ge Tan
1 2 3 4 5 6 7 8 9 10 | data(MA0003.2)
pwm <- toPWM(MA0003.2)
library(CNEr)
axtFilesHg19DanRer7 <- file.path(system.file("extdata", package="TFBSTools"),
"hg19.danRer7.net.axt")
axtHg19DanRer7 <- readAxt(axtFilesHg19DanRer7)
sitePairSet <- searchAln(pwm, axtHg19DanRer7, min.score="80%",
windowSize=51L, cutoff=0.7, strand="*",
type="any", conservation=NULL, mc.cores=1)
toGRangesList(sitePairSet, axtHg19DanRer7)
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