Peak2genelinks information

[maxglenwall]

I´m trying to set up [ShinyArchRUiO] on local, it is not plotting motif matrix UMAPS optimally,. windows are not getting adjusted i was Is it possible to download peak2 gene links information where using shinyArchRUiO e.g

Peak chromosome	Peak start	Peak end	Gene ID	Gene symbol	Gene TSS position	Gene strand	Distance peak to TSS	correlation	p-value	FDR adjusted p-value

Thanks in advance.

[ankushs0128]

Hope this helps

ArchRproject <- addPeak2GeneLinks(
    ArchRProj = ArchRproject,
    reducedDims = "IterativeLSI",
    useMatrix = "GeneIntegrationMatrix"
    )
p2g <- getPeak2GeneLinks(
    ArchRProj = ArchRproject,
    corCutOff = 0.45,
    resolution = 1,
    returnLoops = FALSE
)
p2g
metadata(p2g)
metadata(p2g)$seATAC

p2g$geneName <- mcols(metadata(p2g)$geneSet)$name[p2g$idxRNA]
tssgenes<- as.data.frame(metadata(p2g)$geneSet)
colnames(tssgenes)[2] <- "StartTSS"
colnames(tssgenes)[3] <- "EndTSS"
p2g$peakName <- (metadata(p2g)$peakSet %>% {paste0(seqnames(.), "_", start(.), "_", end(.))})[p2g$idxATAC]
temp1=as.data.frame(p2g)
temp  <- strsplit(p2g$peakName, "_")
temp <- matrix(unlist(temp), ncol=3, byrow=TRUE)
temp <- as.data.frame(temp)
temp1$chr <- temp$V1
temp1$start <- temp$V2
temp1$end <- temp$V3
mergedp2g <- merge(temp1,tssgenes ,by.x="geneName", by.y= "name")
mergedp2g$peakCentre=as.numeric(mergedp2g$start)+250
mergedp2g$looplength=as.numeric(mergedp2g$StartTSS)-as.numeric(mergedp2g$peakCentre)

write.table(mergedp2g,"__peak2genelinks_corr_0.45_res-1_loopobject.txt")