specific peak2gene link

[rojinsafavi]

I wanted to see if there is a way to show a specific peak2gene correlation link in the browser?

1. adding the peak2gene correlation

projHeme2 <- addPeak2GeneLinks(
    ArchRProj = projHeme2,
    reducedDims = "IterativeLSI"
)

2. retrieving the data frame

p2geneDF <- metadata(projHeme2@peakSet)$Peak2GeneLinks
p2geneDF$geneName <- mcols(metadata(p2geneDF)$geneSet)$name[p2geneDF$idxRNA]
p2geneDF$peakName <- (metadata(p2geneDF)$peakSet %>% {paste0(seqnames(.), "_", start(.), "_", end(.))})[p2geneDF$idxATAC]


p2geneDF = as.data.frame(p2geneDF)
p2geneDF = na.omit(p2geneDF)

S = strsplit(p2geneDF[,c('peakName')], '_')
S = as.data.frame(S)
S = t(S)
rownames(S) = seq(1, length(rownames(S)))

p2geneDF$chr   = S[,1]
p2geneDF$start = S[,2]
p2geneDF$end   = S[,3]

p2geneDF = p2geneDF[,c('chr', 'start', 'end', 'Correlation', 'FDR', 'VarQATAC', 'VarQRNA', 'geneName', 'peakName')]

head(p2geneDF)

dim(p2geneDF)
16728109

Now I'd like to look at this specific peak

chr1_11843973_11844473

but the peak is not there when I return the loop?

[rcorces]

I would imagine this is because you are using returnLoops = TRUE which, combined with resolution is going to alter the coordinates of the loops returned. So the precise coordinates do not match. Try it with returnLoops = FALSE

[rojinsafavi]

Thanks @rcorces - I tried that before but it seems that the function requires a grange obj, for now, I am converting the data frame to the grange and using that - it seems to be working , but it appears that I'm geeting peak2peak visualization instead of peak2 gene? this is the comparison of using the loop vs making my own grange for specific peaks

[rcorces]

I'm not sure I understand. You can try returnLoops = TRUE and resolution = NULL. Otherwise I think I need a reproducible example to help more.

There is another open discussion (#1127) which seems to be reporting something similar but I dont have a way to give specific advice without a reproducible example from the tutorial data