distance2Genes: Calculate relative positions of read-enriched regions...

In CSAR: Statistical tools for the analysis of ChIP-seq data

Description

Calculate relative positions of read-enrichment regions regarding gene position

Usage

distance2Genes(win, gff, t = 1, d1 = -3000, d2 = 1000)

Arguments

win	GRange structure obtained with the function sigWin
gff	Data.frame structure obtained after loading a desired gff file
t	Integer. Only distances of read-enriched regions with a score bigger than t will be considered
d1	Negative integer. Minimum relative position regarding the start of the gene to be considered
d2	Positive integer. Maximum relative position regarding the end of the gene to be considered

Value

data.frame structure where each row represents one relative position, and each column being:

peakName	read-enriched region name
p1	relative position regarding the start of the gene
p2	relative position regarding the end of the gene
gene	name of the gene
le	length (bp) of the gene

Author(s)

Jose M Muino, [e-mail]

References

Muino et al. (submitted). Plant ChIP-seq Analyzer: An R package for the statistcal detection of protein-bound genomic regions.
Kaufmann et al.(2009).Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biology; 7(4):e1000090.

See Also

genesWithPeaks, CSAR-package

Examples

##For this example we will use the a subset of the SEP3 ChIP-seq data (Kaufmann, 2009)
data("CSAR-dataset");
##We calculate the number of hits for each nucleotide posotion for the control and sample. We do that just for chromosome chr1, and for positions 1 to 10kb
nhitsS<-mappedReads2Nhits(sampleSEP3_test,file="sampleSEP3_test",chr=c("CHR1v01212004"),chrL=c(10000))
nhitsC<-mappedReads2Nhits(controlSEP3_test,file="controlSEP3_test",chr=c("CHR1v01212004"),chrL=c(10000))


##We calculate a score for each nucleotide position
test<-ChIPseqScore(control=nhitsC,sample=nhitsS)

##We calculate the candidate read-enriched regions
win<-sigWin(test)


##We calculate relative positions of read-enriched regions regarding gene position
d<-distance2Genes(win=win,gff=TAIR8_genes_test)

CSAR documentation built on Nov. 8, 2020, 6:50 p.m.