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Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column
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
─ Packages ───────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [2] CRAN (R 4.4.0)
Biobase 2.64.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
BiocGenerics * 0.50.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
BiocIO 1.14.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
BiocParallel 1.38.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
Biostrings 2.72.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
bitops 1.0-7 2021-04-24 [2] CRAN (R 4.4.0)
cachem 1.1.0 2024-05-16 [2] CRAN (R 4.4.0)
cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.0)
codetools 0.2-20 2024-03-31 [2] CRAN (R 4.4.0)
colorspace 2.1-0 2023-01-23 [2] CRAN (R 4.4.0)
crayon 1.5.3 2024-06-20 [1] CRAN (R 4.4.0)
DelayedArray 0.30.1 2024-05-07 [2] Bioconductor 3.19 (R 4.4.0)
devtools * 2.4.5 2022-10-11 [2] CRAN (R 4.4.0)
digest 0.6.36 2024-06-23 [1] CRAN (R 4.4.0)
dplyr * 1.1.4 2023-11-17 [2] CRAN (R 4.4.0)
ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.4.0)
fansi 1.0.6 2023-12-08 [2] CRAN (R 4.4.0)
fastmap 1.2.0 2024-05-15 [2] CRAN (R 4.4.0)
fs 1.6.4 2024-04-25 [2] CRAN (R 4.4.0)
generics 0.1.3 2022-07-05 [2] CRAN (R 4.4.0)
GenomeInfoDb * 1.40.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
GenomeInfoDbData 1.2.12 2024-05-18 [2] Bioconductor
GenomicAlignments 1.40.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
GenomicRanges * 1.56.0 2024-05-01 [2] Bioconductor 3.19 (R 4.4.0)
getopt 1.20.4 2023-10-01 [2] CRAN (R 4.4.0)
ggcoverage * 1.4.1 2025-02-06 [1] Github (showteeth/ggcoverage@6cd38ab)
ggh4x 0.3.0 2024-12-15 [1] CRAN (R 4.4.0)
ggpattern * 1.1.4 2025-01-29 [1] CRAN (R 4.4.0)
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glue 1.7.0 2024-01-09 [2] CRAN (R 4.4.0)
gridExtra 2.3 2017-09-09 [2] CRAN (R 4.4.0)
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magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.4.0)
Matrix 1.7-0 2024-03-22 [2] CRAN (R 4.4.0)
MatrixGenerics 1.16.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
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memoise 2.0.1 2021-11-26 [2] CRAN (R 4.4.0)
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profvis 0.3.8 2023-05-02 [2] CRAN (R 4.4.0)
promises 1.3.0 2024-04-05 [2] CRAN (R 4.4.0)
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R6 2.5.1 2021-08-19 [2] CRAN (R 4.4.0)
Rcpp 1.0.12 2024-01-09 [2] CRAN (R 4.4.0)
RCurl 1.98-1.14 2024-01-09 [2] CRAN (R 4.4.0)
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restfulr 0.0.15 2022-06-16 [2] CRAN (R 4.4.0)
rjson 0.2.21 2022-01-09 [2] CRAN (R 4.4.0)
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Rsamtools 2.20.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
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sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.4.0)
shiny 1.8.1.1 2024-04-02 [2] CRAN (R 4.4.0)
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tibble 3.2.1 2023-03-20 [2] CRAN (R 4.4.0)
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usethis * 2.2.3 2024-02-19 [2] CRAN (R 4.4.0)
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vctrs 0.6.5 2023-12-01 [2] CRAN (R 4.4.0)
withr 3.0.0 2024-01-16 [2] CRAN (R 4.4.0)
XML 3.99-0.16.1 2024-01-22 [2] CRAN (R 4.4.0)
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XVector 0.44.0 2024-04-30 [2] Bioconductor 3.19 (R 4.4.0)
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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
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?
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 ]
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.
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
