查找点到范围的重叠

Question

我有一个数据框 df1:

df1 <- read.table(text=" Chr06  79641   
Chr06   82862   
Chr06   387314  
Chr06   656098  
Chr06   678491  
Chr06   1018696", header=FALSE, stringsAsFactors=FALSE)

我想检查 df1 中的每一行是否包含在 df2 的范围内。 df2 中的 column2 是范围的开始，column3 是范围的结束。范围之间（行之间）没有重叠。 df2 中的数据按 Column1 和 column2 排序。我为此写了一个循环，但我对此并不满意，因为如果我在 df1 中有几千行，它会运行很长时间。我想找到一种更有效的方法来完成这项工作（最好不要循环）。谢谢。 df2 数据框：

df2 <- read.table(text=" Chr05  799 870
Chr06   77914   77942
Chr06   78233   78269
Chr06   78719   78836
Chr06   79720   87043
Chr06   87223   87305
Chr06   380020  380060
Chr06   387314  387371
Chr06   654907  654988
Chr06   657929  658057
Chr06   677198  677229
Chr06   679555  680170
Chr06   1015425 1015475
Chr06   1018676 1018736
Chr06   1020564 1020592", header=FALSE, stringsAsFactors=FALSE)

我的脚本：

df1$V3 <- FALSE
for (i in 1:dim(df1)[1]) {
  for (j in 1:dim(df2)[1]) {
    if ((df1[i,1] == df2[j,1]) && (df1[i,2]>=df2[j,2]) 
        && (df1[i,2]<=df2[j,3])) {
      df1[i,3]<-TRUE
      break;
    }
  }
}
df1

预期结果显示为df1。

Answer 1

您可以使用 sapply:

sapply(1:nrow(df1), function(x) any(df1[x,2] >= df2$V2 &
                                    df1[x,2] <= df2$V3 &
                                    df1[x, 1] == df2$V1))
[1] FALSE  TRUE  TRUE FALSE FALSE  TRUE

Answer 2

使用GenomicRanges:

#Convert to Granges objects
gr1 <- GRanges(seqnames = df1$V1,
               ranges = IRanges(df1$V2, df1$V2))

gr2 <- GRanges(seqnames = df2$V1,
               ranges = IRanges(df2$V2, df2$V3))
#Subset gr1
subsetByOverlaps(gr1, gr2)

# GRanges object with 3 ranges and 0 metadata columns:
#       seqnames             ranges strand
#          <Rle>          <IRanges>  <Rle>
#  [1]    Chr06 [  82862,   82862]      *
#  [2]    Chr06 [ 387314,  387314]      *
#  [3]    Chr06 [1018696, 1018696]      *
#   -------
#   seqinfo: 1 sequence from an unspecified genome; no seqlengths

#Or we can use merge
mergeByOverlaps(gr1, gr2)

# DataFrame with 3 rows and 2 columns
#                          gr1                        gr2
#                    <GRanges>                  <GRanges>
# 1 Chr06:*:[  82862,   82862] Chr06:*:[  79720,   87043]
# 2 Chr06:*:[ 387314,  387314] Chr06:*:[ 387314,  387371]
# 3 Chr06:*:[1018696, 1018696] Chr06:*:[1018676, 1018736]

此外，查看 bedtools:

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Answer 3

这里有一个 data.table 解决方案作为 GenomicRanges 的替代方案：

library(data.table)
dt1 <- data.table(df1)[, V3 := V2]
dt2 <- data.table(df2, key = c("V2", "V3"))
foverlaps(dt1, dt2)[V1 == i.V1][, -c(4, 6), with = F]
#       V1      V2      V3    i.V3
# 1: Chr06   79720   87043   82862
# 2: Chr06  387314  387371  387314
# 3: Chr06 1018676 1018736 1018696

查找点到范围的重叠

Find point-to-range overlaps

r

bioinformatics