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Ryan C. Thompson
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@ryan-c-thompson-5618
Last seen 5 weeks ago
Icahn School of Medicine at Mount Sinai…
I'm trying to import some of my BED files, and rtracklayer is choking because it expects an integer where my files have floating point values:
> x <- import(sprintf("data_files/ChIP-Seq/H3K4me3_peaks_IDR_filtered.bed"))
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
scan() expected 'an integer', got '16.25851'
> traceback()
8: scan(file = file, what = what, sep = sep, quote = quote, dec = dec,
nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE,
fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip,
multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes,
flush = flush, encoding = encoding, skipNul = skipNul)
7: read.table(con, colClasses = bedClasses, as.is = TRUE, na.strings = ".",
comment.char = "")
6: DataFrame(read.table(con, colClasses = bedClasses, as.is = TRUE,
na.strings = ".", comment.char = ""))
5: .local(con, format, text, ...)
4: import(FileForFormat(con), ...)
3: import(FileForFormat(con), ...)
2: import(sprintf("data_files/ChIP-Seq/H3K4me3_peaks_IDR_filtered.bed"))
1: import(sprintf("data_files/ChIP-Seq/H3K4me3_peaks_IDR_filtered.bed"))
>
Here's what the first few lines of that file look like:
$ head "data_files/ChIP-Seq/H3K4me3_peaks_IDR_filtered.bed" chr1 27510 30426 H3K4me3_peak_5 800 * 16.25851 80.02037 -1 1703 chr1 540149 541537 H3K4me3_peak_22 145 * 4.97981 14.53762 -1 426 chr1 713117 714018 H3K4me3_peak_28 1277 * 25.02645 127.71224 -1 770 chr1 714191 716308 H3K4me3_peak_29 602 * 14.99855 60.24956 -1 427 chr1 760783 762907 H3K4me3_peak_41 711 * 14.27445 71.18283 -1 1761 chr1 763044 765173 H3K4me3_peak_42 198 * 4.9907 19.84909 -1 987 chr1 776489 778099 H3K4me3_peak_51 358 * 9.35653 35.85113 -1 981 chr1 778950 780404 H3K4me3_peak_53 233 * 7.24799 23.38787 -1 1133 chr1 892835 894617 H3K4me3_peak_72 410 * 9.88536 41.03654 -1 1206 chr1 894804 897069 H3K4me3_peak_73 224 * 8.19048 22.41068 -1 101
Is it possible that rtracklayer could be modified to accept floating point values for the relevant columns?
I'm trying out the extraCols argument, and it doesn't seem to be working, although it seems to encounter an error on a different element of the first row:
extraCols_narrowPeak <- c(signalValue = "numeric", pValue = "numeric", qValue = "numeric", peak = "integer") import.narrowPeak <- function(..., ) { import(..., format="BED", extraCols=extraCols_narrowPeak) } > x <- import.narrowPeak("data_files/ChIP-Seq/H3K4me3_peaks_IDR_filtered.bed") Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, (from #2) : scan() expected 'an integer', got '80.02037'Where can I download that file?
I figured out the problem. My function signature above has an extra comma, which somehow resulted in this non sequitur error. After removing the comma, the above function works as expected.
Hi Ryan, I encounter the same your problem, could you please tell me where is the extra comma causing the problem and how it should be?
thank you
Ryan has not been seen for some time, and this thread is almost 5 years old. You may consider creating a new question, and also providing a minimal reproducible example for others.
The third line is
but should be
Yes, these are derived from narrowPeak MACS2 output files. Good to know that rtracklayer has support for them.