countmotifsegreads: Calculate numbers of reads overlapping motif sites
In spo111/DynaMO: DynaMO predicts spatiotemporal binding of transcription factors

Description Usage Arguments Details Value Author(s) Examples

Count numbers of reads overlapping motif sites.

1 2	countmotifsegreads(read, segmentfile, seqL=150, core=1, format="bam", histonemotifRFid, readsmem)

`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.

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.

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.

Zheng Kuang

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)