CODEWITHSUNDEEP
rdataframebioinformatics
Fpertille
Fpertille

Reputation: 383

How to transform a range into individual positions

I have a huge "range" data, this data is in GenomicRanges format, if I convert this to data.frame, follows one example:

file <- "seqnames start end width strand 
chr1  2  5  4      *
chr2  3  7  5      *"
file<-read.table(text=file,header=T)

I would like to decompose this "ranges" in individual positions like this example:

file2 <- "seqnames Position 
chr1  2
chr1  3
chr1  4
chr1  5
chr2  3
chr2  4
chr2  5
chr2  6
chr2  7"

file2 <- read.table(text=file2,header=T)

How can I do this?

Upvotes: 1

Views: 157

Answers (2)

dww
dww

Reputation: 31452

We can use data.table

library(data.table)
setDT(file)[, .(position = start:end), by = seqnames]

#    seqnames position
# 1:     chr1        2
# 2:     chr1        3
# 3:     chr1        4
# 4:     chr1        5
# 5:     chr2        3
# 6:     chr2        4
# 7:     chr2        5
# 8:     chr2        6
# 9:     chr2        7

Upvotes: 1

Martin Morgan
Martin Morgan

Reputation: 46856

If using Bioconductor GenomicRanges, then

> GPos(GRanges(c("chr1:2-5", "chr2:3-7")))
GPos object with 9 positions and 0 metadata columns:
      seqnames       pos strand
         <Rle> <integer>  <Rle>
  [1]     chr1         2      *
  [2]     chr1         3      *
  [3]     chr1         4      *
  [4]     chr1         5      *
  [5]     chr2         3      *
  [6]     chr2         4      *
  [7]     chr2         5      *
  [8]     chr2         6      *
  [9]     chr2         7      *
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths

perhaps first with

GRanges(file)

Upvotes: 2

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