在GenomicRanges中查找岛屿

Question

在GenomicRanges中，一个有趣的问题是基因岛的识别。

我正在尝试寻找相邻范围不超过特定距离的最大范围子集。为了解决这个问题，我尝试根据各个范围之间的差异来分配组。

我在IRanges包中搜索了合适的方法，但到目前为止还没有成功。

daf <- data.frame(seqnames="ConA",start=c(10,39,56,1000,5000),end=c(19,44,87,1100,5050),ID=paste0("Range",LETTERS[1:5]))
gr <- makeGRangesFromDataFrame(daf,keep.extra.columns=TRUE)
## Order the data frame by start column
oo <- order(daf$start)
daf <- daf[oo,]

# Calculate the distance
dd <- c(0,diff(daf$start))
daf$diff <- dd
daf$group <- rep(1,nrow(daf))

group <- 1
for(i in 1:nrow(daf)){
  if(daf$diff[i] > 500){
    group <- group + 1
  }
  daf$group[i] <- group
}

根据所分配的组，可以找到最大的组。您是否知道更好的解决方案，避免for循环？

Answer 1

我相信这会在没有循环的情况下完成您所期望的事情：

## Load library
library(GenomicRanges)

## Create the data
gr <- GRanges(seqnames="ConA",
              ranges=IRanges(start=c(10,39,56,1000,5000),
                             end=c(19,44,87,1100,5050),
                             names = paste0("Range",LETTERS[1:5])))

## Get the "start sites" = TSS.
## Use the promoters function if you need to take the strand into account:
grTSS <- promoters(gr, upstream = 0, downstream = 1)

## Create islands in which start sites are located less than 500bp apart
## If distance between start sites is <500bp then ranges of size 501bp centered on start sites overlap
islands <- reduce(grTSS + 250, ignore.strand = TRUE)
names(islands) <- paste0("island", 1:length(islands))

## Get the link between start sites and islands:
ovl <- findOverlaps(grTSS, islands, type = "within", ignore.strand = TRUE)

## Add the group info in the original GRanges object:
gr$group <- names(islands)[subjectHits(ovl)] 

在创建孤岛时可以考虑链信息：islands <- reduce(grstarts + 250, ignore.strand = FALSE)

我们可以直接使用基因边界(开始和结束)，而不是只关注起始点/ TSS：islands <- reduce(gr + 250, ignore.strand = TRUE)

希望这能有所帮助