Dear all,

I would need a simple suggestion : I am using AUTOPLOT function in GGBIO
package in order to display a set of ChIP-seq peaks in a specific region
(chr-start-end).

I am reading the set of ChIP-seq peaks in BED format, please could you let
me know how I could  display the data only in the specific region
(chr-start-end).

The R code I am using is :

-------------------to specify the region -------------------
chr <-"chr2"
start <- 10898631
end <- 11859944
region <- GRanges(chr, IRanges(start,end))

--------------------to read the file with ChIP-seq peaks ----------------

er<-read.delim("ChIP-seq.peaks",header=TRUE)
er_ranges <-
GRanges(seqnames=er$chr,IRanges(er$start,er$end),strand="*",score=er$intensity)

--------------------------to display the data in the region "region"
---------------------

er_plots <- autoplot(er_ranges,geom="bar",aes(col=score)) + xlim(start,end)

OR

er_plots <- autoplot(er_ranges,geom="bar",which = regionb, stat =
"identity", color = "blue", fill = "blue")

-------------------------------------------------------------------------------------------------------------

thank you very much !

Bogdan

	[[alternative HTML version deleted]]

