toGRangesList-methods: toGRangesList function

In ge11232002/TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

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)

ge11232002/TFBSTools documentation built on Sept. 12, 2021, 12:07 p.m.