toGRangesList-methods {TFBSTools} | R Documentation

## toGRangesList function

### Description

Get the genomic coordinates from SitePairSetList.

### Value

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.

### Methods

`signature(x = "SitePairSetList", axt = "Axt")`

  Convert the relative coordinates to absolute coordinates.

### Author(s)

Ge Tan

### Examples

      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)

[Package TFBSTools version 1.18.0 Index]