get.motif: Read motif sites

In spo111/DynaMO: DynaMO predicts spatiotemporal binding of transcription factors

Description

Read a file containing locations of motif sites and convert it into a GRanges object.

Usage

get.motif(file, extendL)

Arguments

file	The name of the file where the locations of motif sites are stored.
extendL	A integer. The length to be extended from the centers of motif sites.

Details

The function reads a file containing locations of motif sites and converts it to a GRanges object. Because real binding sites are often located near peaks of histone modifications but not in the middle of peaks. By extending motif sites by 200 to 1000 bp on both sides, DynaMO can capture real motif sites.

Value

A GRanges object.

Author(s)

Zheng Kuang

Examples

readfile<-system.file("extdata","motif_1.txt",package="DynaMO",mustWork=TRUE)
motif1<-get.motif(readfile,300)

spo111/DynaMO documentation built on May 30, 2019, 7:59 a.m.