countmotifsegreads: Calculate numbers of reads overlapping motif sites

Description Usage Arguments Details Value Author(s) Examples

View source: R/DynaMO.R

Description

Count numbers of reads overlapping motif sites.

Usage

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countmotifsegreads(read, segmentfile, seqL=150, core=1, format="bam",
histonemotifRFid, readsmem)

Arguments

read

A list object where each element is a GRanges object storing read coordinates of one sample, or a data.frame object where each row is the path to a file storing aligned reads of one sample.

segmentfile

A list object where each element is a GRanges object storing the locations of motif sites from one motif.

seqL

The length to be extended from the 5' ends of reads.

core

The number of cores to use.

format

The format of aligned reads. The format can be a .txt file or a .bam file.

histonemotifRFid

The list object where each element contains the indexes of motif sites for read counting. The indexes are also used to name the motif sites.

readsmem

A logcial. If TRUE, aligned reads are imported once and kept in memory. It requires large memory but saves time.

Details

The function calculates the numbers of reads overlapping motif sites. Motif sites from different motifs are stored in a list object. If multiple samples of aligned reads are provided, read counts are normalized by total number of reads across samples.

Value

A list object with two elements. The first is a list object where each element is a matrix of normalized read counts at motif sites. Each row is the read counts at one motif site and each column is one sample. The second is a vector of ratios normalized by total number of reads across samples.

Author(s)

Zheng Kuang

Examples

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readfile<-system.file("extdata","read1.txt",package="DynaMO",mustWork=TRUE)
read1<-get.reads(readfile,150,"txt")
readfile<-system.file("extdata","motif_1.txt",package="DynaMO",mustWork=TRUE)
motif1<-get.motif(readfile,300)
motifreads<-countmotifsegreads(list(read1),list(motif1),150,1,"txt",
list(1:length(motif1)),T)

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