get.reads: Import aligned reads

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

Description

Read a file containing aligned reads and convert it into a GRanges object.

Usage

get.reads(file, seqL, readformat)

Arguments

file	The name of the file where the aligned reads are stored.
seqL	The length to be extended from the 5' ends of reads.
readformat	The format of read files. The format can be a .txt file or a .bam file.

Details

The purpose of this function is to import aligned reads and convert to GRanges objects. Two formats can be recognized by this function, a .txt file or a .bam file. Three columns separated by tabs are expected in a .txt file. The first column stores chromosome name. The second column stores left end coordinates of reads and the third column stores the strands of reads. seqL equals to the size of DNA fragments, and usually ranges from 150 to 300.

Value

A GRanges object.

Author(s)

Zheng Kuang

Examples

readfile<-system.file("extdata","read1.txt",package="DynaMO",mustWork=TRUE)
read1<-get.reads(readfile,150,"txt")

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