R/getFlankingGene.R

In YuLab-SMU/ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

##' @import IRanges
##' @importFrom dplyr mutate
##' @importFrom dplyr group_by
getAllFlankingGene <- function(peak.gr, features, level="transcript", distance=5000) {
    peak.gr2 <- peak.gr
    start(ranges(peak.gr)) = start(ranges(peak.gr)) - distance
    end(ranges(peak.gr)) = end(ranges(peak.gr)) + distance
    hit <- findOverlaps(peak.gr, unstrand(features))
    qh <- queryHits(hit)
    sh <- subjectHits(hit)
    
    featureHit <- features[sh]
    names(featureHit)=NULL
    hitInfo <- as.data.frame(featureHit)

    if (level == "transcript") {
        eg <- TXID2EG(featureHit$tx_id, geneIdOnly=TRUE)
        hitInfo$geneId <- eg
    } else {
        cn <- colnames(hitInfo)
        colnames(hitInfo)[cn == "gene_id"] <- "geneId"
    }


    hitInfo$peakIdx <- qh

    overlapHit <- findOverlaps(peak.gr2, unstrand(featureHit))
    hitInfo$distance <- NA
    hitInfo$distance[subjectHits(overlapHit)] <- 0

    psD <- ifelse(strand(featureHit) == "+",
                  start(peak.gr2[qh]) - start(featureHit),
                  end(featureHit)-end(peak.gr2[qh]))
    
    peD <- ifelse(strand(featureHit) == "+",
                  end(peak.gr2[qh]) - start(featureHit),
                  end(featureHit)-start(peak.gr2[qh]))

    idx <- abs(psD) > abs(peD)
    dd <- psD
    dd[idx] <- peD[idx]

    ii <- is.na(hitInfo$distance)
    hitInfo$distance[ii] <- dd[ii]

    peakIdx <- tx_name <- geneId <- distance <- NULL

    if (level == "transcript") {
        hitInfo2 <- group_by(hitInfo, peakIdx) %>%
            mutate(flank_txIds=paste(tx_name, collapse=";"),
                   flank_geneIds=paste(geneId, collapse=";"),
                   flank_gene_distances=paste(distance, collapse=";"))
        res <- hitInfo2[,c("peakIdx", "flank_txIds", "flank_geneIds", "flank_gene_distances")]
        res$flank_txIds <- as.character(res$flank_txIds)
    } else {
        hitInfo2 <- group_by(hitInfo, peakIdx) %>%
            mutate(flank_geneIds=paste(geneId, collapse=";"),
                   flank_gene_distances=paste(distance, collapse=";"))
        res <- hitInfo2[,c("peakIdx", "flank_geneIds", "flank_gene_distances")]
    }

    res <- unique(res)
    res$flank_geneIds <- as.character(res$flank_geneIds)
    res$flank_gene_distances <- as.character(res$flank_gene_distances)
    
    return(res)    
}