motifRFid: Find motif sites for training random forest models

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

Description

Find ids of positive, negative and background motif sites of each motif for training random forest models.

Usage

motifRFid(motifseg, histonemotifsegreads, motifpeakoverlap, motifseg500overlapid)

Arguments

motifseg	A list object where each element is a GRanges object storing the locations of motif sites from one motif.
histonemotifsegreads	A list object with length equal to the number of histone markers and each element is a list object with length equal to the number of motifs where each sub-element is a matrix storing read counts of one histone modification at motif sites from different motifs. Columns of matrices are read counts from different samples and rows are different motif sites.
motifpeakoverlap	A list object with length equal to the number of histone markers and each element contains overlapping information of motif sites and one marker. Each element is a list object with length equal to the number of motifs and each sub-element is a matrix containing overlapping information of motif sites from one motif. Each column of the matrix is the numbers of peaks overlapping each motif site.
motifseg500overlapid	A list object with length equal to the number of motifs. Each element is a vector of numbers of peaks overlapping motif sites from this motif.

Details

This function finds motif sites for training random forest models. It identifies at most 250 motif sites from each motif which overlap peaks of at least one histone marker as positive sites and 250 motif sites which don't overlap any peak from any histone marker as negative sites. It also identifies 250 motif sites as background sites for each motif.

Value

It returns a list with length equal to the number of motifs and each element is another list with length equal to the number of samples. Each list is another list of 3 elements. The first is the id of positive motif sites and the second is the id of negative motif sites and the third is the id of background sites.

Author(s)

Zheng Kuang

Examples

#Prepare motifseg reads
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)))
#Detect peaks
library(BayesPeak)
readfile<-system.file("extdata","read1.txt",package="DynaMO",mustWork=TRUE)
tempreads<-get.reads(readfile,150,"txt")
tempreads1=as.data.frame(tempreads)
tempreads2=cbind(tempreads1[,1:3],tempreads1[,5])
colnames(tempreads2)=c("chr","start","end","strand")
temppeak=summarize.peaks(bayespeak(tempreads2))
peak=GRanges(seqnames=Rle(as.character(space(temppeak))),
ranges=IRanges(start=start(temppeak),end=end(temppeak)))
#Count overlaps of motif sites and peaks
motifpeakoverlap=data.matrix(countOverlaps(motif1,peak))
#motifRFid
motifid1=motifRFid(list(motif1),list(motifreads),list(list(motifpeakoverlap)),
list(1:1000))

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