Entering edit mode
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$end),strand="*",score=er$i
ntensity)
--------------------------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
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