Peak2Gene links limited to one gene

[NoemieL]

Hi,
I am interested in looking at peaks to a specific gene but in a big window. I adapted the upstream and downstream parameters in consequences. However I get the peak to gene links that are not related to the gene I mention in the geneSymbol parameter. How can I get rid of these links?

Thanks

[rcorces]

Sorry. I dont understand the question. I dont know what you want to do and I dont know what you mean by "the geneSymbol parameter". Please provide an example using the tutorial data if you would like help.

[NoemieL]

Sorry Ryan if I was not clear. I want the peak2Gene links that are specific to a gene. By increasing the window to get the peak2Gene that could be far from this gene, I also get the peak2Gene that are associated to other genes from this window. So I get a lot of unwanted peak2Gene links. How could I get rid of these unwanted links?

For exemple, I am interested by the gene MCL1, as you could see on the attached track plot that I obtained with the following command, there are peak2Gene links that are associated to ADAMTSL4 or ENSA. How could I remove these links from the track plot?
"'
p2g <- getPeak2GeneLinks(
ArchRProj = ArchRProject,
corCutOff = 0.45,
resolution = 10000,
returnLoops = TRUE
)

p <- plotBrowserTrack(
ArchRProj = ArchRProject,
groupBy = "ID",
geneSymbol = "MCL1",
upstream = 50000,
downstream = 50000,
loops = getPeak2GeneLinks(ArchRProject),
sizes = c(10, 1,2,2),
pal=pal_ID
)
"'

[rcorces]

just take the output of getPeak2GeneLinks(ArchRProject), subset it by loops that overlap your promoter or region of interest, and pass that plotBrowserTrack()

[NoemieL]

Thanks a lot, I will try that!

[YesseniaCQ]

Thanks a lot, I will try that!

Hi,did you kown how to achieve now?