Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column

[pcantalupo]

Hello,

I'm trying to load a track file (bigWig) but am getting an error. The bigWig file comes from nfcore/rnaseq pipeline and is created by the UCSC program bedGraphtoBigWig. You can see that my SampleName matches the prefix of the bigWig filename. Not sure what I'm doing wrong.

Thank you

metadata = read.delim(opts$samplesheet)
metadata
            SampleName Type Group
1 24hpi_Dunlop.forward    A     B

list.files(opts$folder, pattern = metadata$SampleName)
[1] "24hpi_Dunlop.forward.bigWig"

track = LoadTrackFile(track.folder = opts$folder, format = "bw",
                      region = "chr16:67192155-67198918", meta.info = metadata)
Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column

packageVersion("ggcoverage")
[1] ‘1.4.1’


> devtools::session_info()
─ Session info ───────────────────────────────────────────────
 setting  value
 version  R version 4.4.0 (2024-04-24)
 os       Red Hat Enterprise Linux
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2025-02-06
 rstudio  2023.03.0+386 Cherry Blossom (server)
 pandoc   2.5 @ /ihome/crc/install/pandoc/pandoc-2.5/bin/pandoc

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 [1] /ihome//R/x86_64-pc-linux-gnu-library/4.4
 [2] /ihome/crc/install/gcc-12.2.0/r/4.4.0/lib64/R/library

[m-jahn]

Hi! Have you found a solution for the problem?
if not, can you provide a reproducible example, maybe with a reduced example file of your data?

[pcantalupo]

No luck.

You can try any one of the BigWig files from the example output of the nfcore-rnaseq pipeline. I just tried the GM12878_REP1.forward.bigWig file found here https://nf-co.re/rnaseq/3.18.0/results/rnaseq/results-b96a75361a4f1d49aa969a2b1c68e3e607de06e8/aligner_star_salmon/star_salmon/bigwig/ and it failed with the same error:

> metadata = data.frame(SampleName = c("GM12878_REP1.forward"), Type = "A", Group = "B")
> metadata
            SampleName Type Group
1 GM12878_REP1.forward    A     B
> list.files(".", pattern = metadata$SampleName)
[1] "GM12878_REP1.forward.bigWig"
> track = LoadTrackFile(track.folder = ".", format = "bw",
+                       region = "16:67192155-67198918", meta.info = metadata)
Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column
> packageVersion("ggcoverage")
[1] ‘1.4.1’

[ P.S. I edited my original post...changed "chr16" to "16" to match the genome naming. You still get the error either way ]

[m-jahn]

I think it is because of the file ending. Can you to rename that file to end with .bw instead of .bigwig?
Currently ggcoverage is quite strict when it comes to file formats.

[m-jahn]

If this is the problem I will push a fix that will allow different variations of file endings and give a warning for non-comploiant files.

edit: I can reproduce the error when using .bigwig

[danhtruong]

I also renamed from .bigwig to .bw and it worked.

[m-jahn]

I made a fix for this that will be merged soon.