reading a bed file in R

Question

[zizigolu]

hi,

I have a bed file like below

FLP1    252    1523
RAF1    3271    3816
REP1    1887    3008
REP2    5308    6198

I was reading the file in R

bed <- as.data.frame(read.table("file.bed",header = FALSE, sep="\t",stringsAsFactors=FALSE))
Warning messages:
1: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  EOF within quoted string
2: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  number of items read is not a multiple of the number of columns

but when I read file as csv no error anymore

how I can read this file as table please?

thank you

Answer 1

[spleonard1]

Maybe you have a weird hidden character in there somewhere. try adding

quote = ""

to your initial read.table call, like:

bed <- as.data.frame(read.table("file.bed",header = FALSE, sep="\t",stringsAsFactors=FALSE, quote=""))

[Charles Plessy]

Actually, as.data.frame() is not needed: read.table() will already return a data frame.

> bed <- read.table("file.bed",header = FALSE, sep="\t",stringsAsFactors=FALSE, quote="")

> bed
    V1   V2   V3
1 FLP1  252 1523
2 RAF1 3271 3816
3 REP1 1887 3008
4 REP2 5308 6198

> as.data.frame(bed)
    V1   V2   V3
1 FLP1  252 1523
2 RAF1 3271 3816
3 REP1 1887 3008
4 REP2 5308 6198

> identical(bed, as.data.frame(bed))
[1] TRUE

[zizigolu]

thank you very much

[zizigolu]

thank you so much

my file was read by your comment

Answer 2

[Giovanni M Dall'Olio]

The most versatile option is to use the import function from rtracklayer:

> source("https://bioconductor.org/biocLite.R")
> biocLite("rtracklayer")
> library(rtracklayer)
> import("example.txt", format="bed")
GRanges object with 9 ranges and 4 metadata columns:
      seqnames                 ranges strand |        name     score
         <Rle>              <IRanges>  <Rle> | <character> <numeric>
  [1]     chr7 [127471197, 127472363]      + |        Pos1         0
  [2]     chr7 [127472364, 127473530]      + |        Pos2         0
  [3]     chr7 [127473531, 127474697]      + |        Pos3         0
  [4]     chr7 [127474698, 127475864]      + |        Pos4         0
  [5]     chr7 [127475865, 127477031]      - |        Neg1         0
  [6]     chr7 [127477032, 127478198]      - |        Neg2         0
  [7]     chr7 [127478199, 127479365]      - |        Neg3         0
  [8]     chr7 [127479366, 127480532]      + |        Pos5         0
  [9]     chr7 [127480533, 127481699]      - |        Neg4         0

The import() function can be used to read most common bioinformatics format: bed, gtf, wig, bigwig, etc..

[zizigolu]

thank you

import("footprint.txt", format="bed")
Error: could not find function "import"

[Giovanni M Dall'Olio]

sorry, you have to load the rtracklayer library first.

[zizigolu]

thank you Giovanni

[zizigolu]

thanks again,

import("footprint.txt", format="bed")
Error in open.connection(con, open) : cannot open the connection
In addition: Warning message:
In open.connection(con, open) :
  cannot open file 'footprint.txt': No such file or directory

[bioinfo8]

Hi,

I am trying to use TEQC package and getting following error:

sample <- get.targets("C:/sample.bed", chrcol = 1, startcol = 2, endcol = 3, zerobased = TRUE, skip = 1, header = FALSE)

Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  solving row 560885: negative widths are not allowed

So I used import() from rtracklayer (https://support.bioconductor.org/p/38219/) but when I try to import, it shows error:

sample <- import("C:/sample.bed", format="bed")

Error: logical subscript contains NAs

My bed file contains scaffold names also in addition to chromosome number in the 1st column, so I think this may be the reason.

However, read.table() works fine.

Kindly guide how I can import bed file including scaffold names in 1st column and use TEQC package.

[zizigolu]

Sorry I am not good in R and always face error in R and this forum is my only source to get help.