toGRangesList-methods {TFBSTools} | R Documentation |
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
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)