[R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserved words. this is not the case
Hello Biostars,
converting dataframe to Granges object using GenomicRanges::makeGRangesFromDataFrame but keeeps failing due to presumably reserved names in metadata column
but my metadata columns do not contain these
"seqnames", "ranges", "strand", "seqlevels", "seqlengths", "isCircular", "start", "end", "width"
any suggestions on how to resolve this would be greatly appreciated.
thanks
library(GenomicFeatures)
GenomicRanges::makeGRangesFromDataFrame(df=merged.biomart.hg19.cna,
seqnames.field="seqnames",
start.field="start",
end.field="end",
strand.field="strand",
keep.extra.columns = T, ignore.strand=TRUE)
Error in validObject(ans) : invalid class “GRanges” object:
names of metadata columns cannot be one of "seqnames", "ranges", "strand", "seqlevels", "seqlengths", "isCircular", "start", "end", "width",
#showing colnames
colnames(merged.biomart.hg19.cna)
[1] "seqnames" "start" "end" "strand" "Gene.stable.ID" "Biomart_str" "Gene.name" "HGNC.symbol" "Gene.type"
[10] "copy_number" "P13_HER2_GU" "P05_LumA_G2" "P12_HER2_G3" "P11_LumA_G2" "P10_TNBC_G3" "P09_LumA_G3" "P14_LumA_G3" "P15_TNBC_GU"
[19] "P06_LumB_G3" "P01_TNBC_G3" "P04_LumA_G3" "P02_TNBC_G3" "P07_LumA_G3" "P03_TNBC_G2" "P08_HER2_GU"
#showing traceback()
traceback()
4: stop(msg, ": ", errors, domain = NA)
3: validObject(ans)
2: GRanges(ans_seqnames, ans_ranges, strand = ans_strand, ans_mcols,
seqinfo = ans_seqinfo)
1: GenomicRanges::makeGRangesFromDataFrame(df = merged.biomart.hg19.cna,
seqnames.field = "seqnames", start.field = "start", end.field = "end",
strand.field = "strand", keep.extra.columns = T, ignore.strand = TRUE)
"element"
##showing session info
sessionInfo()
R version 4.0.1 (2020-06-06)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] RColorBrewer_1.1-2 reshape2_1.4.4 ggpubr_0.3.0 reshape_0.8.8 forcats_0.5.0 stringr_1.4.0
[7] dplyr_1.0.0 purrr_0.3.4 readr_1.3.1 tidyr_1.1.0 tibble_3.0.1 ggplot2_3.3.1
[13] tidyverse_1.3.0 dendextend_1.13.4 plot.matrix_1.4 pheatmap_1.0.12 data.table_1.12.8 AnnotationHub_2.20.0
[19] BiocFileCache_1.12.0 dbplyr_1.4.4 GenomicFeatures_1.40.0 AnnotationDbi_1.50.0 Biobase_2.48.0 biomaRt_2.44.0
[25] GenomicRanges_1.40.0 GenomeInfoDb_1.24.0 IRanges_2.22.2 S4Vectors_0.26.1 BiocGenerics_0.34.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 ggsignif_0.6.0 ellipsis_0.3.1 rio_0.5.16 XVector_0.28.0
[6] fs_1.4.1 rstudioapi_0.11 farver_2.0.3 bit64_0.9-7 interactiveDisplayBase_1.26.3
[11] fansi_0.4.1 lubridate_1.7.9 xml2_1.3.2 jsonlite_1.6.1 Rsamtools_2.4.0
[16] broom_0.5.6 shiny_1.4.0.2 BiocManager_1.30.10 compiler_4.0.1 httr_1.4.1
[21] backports_1.1.7 assertthat_0.2.1 Matrix_1.2-18 fastmap_1.0.1 cli_2.0.2
[26] later_1.1.0.1 htmltools_0.4.0 prettyunits_1.1.1 tools_4.0.1 gtable_0.3.0
[31] glue_1.4.1 GenomeInfoDbData_1.2.3 rappdirs_0.3.1 Rcpp_1.0.4.6 carData_3.0-4
[36] cellranger_1.1.0 vctrs_0.3.1 Biostrings_2.56.0 nlme_3.1-148 rtracklayer_1.48.0
[41] openxlsx_4.1.5 rvest_0.3.5 mime_0.9 lifecycle_0.2.0 rstatix_0.5.0
[46] XML_3.99-0.3 zlibbioc_1.34.0 scales_1.1.1 hms_0.5.3 promises_1.1.1
[51] SummarizedExperiment_1.18.1 yaml_2.2.1 curl_4.3 memoise_1.1.0 gridExtra_2.3
[56] stringi_1.4.6 RSQLite_2.2.0 BiocVersion_3.11.1 zip_2.0.4 BiocParallel_1.22.0
[61] rlang_0.4.6 pkgconfig_2.0.3 matrixStats_0.56.0 bitops_1.0-6 lattice_0.20-41
[66] GenomicAlignments_1.24.0 bit_1.1-15.2 tidyselect_1.1.0 plyr_1.8.6 magrittr_1.5
[71] R6_2.4.1 generics_0.0.2 DelayedArray_0.14.0 DBI_1.1.0 foreign_0.8-80
[76] pillar_1.4.4 haven_2.3.1 withr_2.2.0 abind_1.4-5 RCurl_1.98-1.2
[81] modelr_0.1.8 crayon_1.3.4 car_3.0-8 utf8_1.1.4 viridis_0.5.1
[86] progress_1.2.2 grid_4.0.1 readxl_1.3.1 blob_1.2.1 reprex_0.3.0
[91] digest_0.6.25 xtable_1.8-4 httpuv_1.5.4 openssl_1.4.1 munsell_0.5.0
[96] viridisLite_0.3.0 askpass_1.1
>
• 4,423 views
•
link
updated
by
Kevin Blighe
•
written
by
Alewa
•
written
by
Alewa
1 answer
Thanks @Kevin Blighe,
it turns out the 'strand' column was the source of error. i think because of ignore.strand=TRUE flag in GenomicRanges::makeGRangesFromDataFrame
set ignore.strand=TRUE inistially because GenomicRanges::makeGRangesFromDataFrame wasn't recognizing values in strand column
quick fix was;
makeGRangesFromDataFrame(df = merged.biomart.hg19.cna,
keep.extra.columns = TRUE, ignore.strand = FALSE)
or
merged.biomart.hg19.cna <- merged.biomart.hg19.cna[-4]
makeGRangesFromDataFrame(df = merged.biomart.hg19.cna,
keep.extra.columns = TRUE, ignore.strand = TRUE)
thanks S
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Hey, what is the output of
?
please ignore the lots NA; what we see are pseudogenes
I see - thanks ekwame. The column names should already be okay, so, you should not have to specify them.
I wonder could you simply try:
...or: