error in readPeakFile {chipseeker}
0
0
Entering edit mode
@theodoregeorgomanolis-7993
Last seen 19 days ago
Germany

Hi all, So I got several bed files as created by MACS2. I am loading them as list with the following:

peaks <- as.list(c("K002000291_97925.narrowPeak",
                      "K002000291_97926.narrowPeak",
                      "K002000291_97927.narrowPeak",
                      "K002000291_97928.narrowPeak",
                      "K002000291_97929.narrowPeak",
                      "K002000299_99400.narrowPeak",
                      "K002000299_99401.narrowPeak",
                      "K002000299_99402.narrowPeak",
                      "K002000299_99403.narrowPeak"))
peaks
$K002000291_97925
[1] "K002000291_97925.narrowPeak"

$K002000291_97926
[1] "K002000299_99400.narrowPeak"

this are the same structure as the provided sample files, but not gziped:

files=getSampleFiles()
files
$ARmo_0M
[1] "R/x86_64-pc-linux-gnu-library/3.6/ChIPseeker/extdata/GEO_sample_data/GSM1174480_ARmo_0M_peaks.bed.gz"

$ARmo_1nM
[1] "R/x86_64-pc-linux-gnu-library/3.6/ChIPseeker/extdata/GEO_sample_data/GSM1174481_ARmo_1nM_peaks.bed.gz"

but when I convert them to the GRanges I got the following error:

peak=readPeakFile(peaks)
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  'file' must be a character string or connection

If I use only one part of the list, all is good:

peak=readPeakFile(Goettingen_peaks[[1]])
peak
GRanges object with 34719 ranges and 7 metadata columns:
          seqnames            ranges strand |     MACS_peak_1      X111        .  X7.32948 X14.79510 X11.12669
             <Rle>         <IRanges>  <Rle> |        <factor> <integer> <factor> <numeric> <numeric> <numeric>
      [1]     chr1       11329-11448      * |     MACS_peak_2        25        .   3.76954   5.24804   2.56086
      [2]     chr1       28998-29387      * |     MACS_peak_3       152        .  10.23664  19.19137  15.22631
      [3]     chr1     714087-714492      * |    MACS_peak_10        27        .   4.34309   5.50985   2.78392

but then I am getting another error as also seen in the https://support.bioconductor.org/p/119149/:

covplot(peak = peak, weightCol="V5")
Error in .normarg_shift_or_weight(weight, "weight", x) : 
  'weight' must be a numeric vector, a single string, or a list-like object

any help would be appreciated.

ChIPseeker readPeakFile • 1.6k views
ADD COMMENT
0
Entering edit mode

Looks like the readPeakFile only takes one file at a time? I wrote a for loop to read all the files into Granges format.

Yu also provided a link to use GRangesList instead, which will solve the problem https://guangchuangyu.github.io/2016/02/covplot-supports-grangeslist/

ADD REPLY

Login before adding your answer.

Traffic: 318 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6