*gsa.out: truncated `VARIABLE` names
Closed this issue · 1 comments
bschilder commented
1. Bug description
For some reason, MAGMA decided to truncate the VARIABLE column in their gsa.out files. This screws up attempts to match up the celltype names with those in the CTD.
Not sure if this was always the case, or I'm just noticing now because I'm using some CTDs with long celltype names (e.g. HumanCellLandscape)
Console output
Expected behaviour
MAGMA.Celltyping can read in the results files without hitting an error.
2. Reproducible example
Code
magma_dirs <- MAGMA.Celltyping::import_magma_files(ids = c("ieu-a-298"))
ctd <- MAGMA::get_ctd("ctd_HumanCellLandscape")
res <- MAGMA.Celltyping::celltype_associations_pipeline(
ctd = ctd,
ctd_name ="ctd_HumanCellLandscape",
ctd_species = "human",
magma_dirs = magma_dirs,
run_linear = TRUE,
run_top10 = TRUE,
upstream_kb = 35,
downstream_kb = 10,
force_new = TRUE,
save_dir=here::here("processed_data/MAGMA")) 3. Session info
R Under development (unstable) (2023-03-02 r83926)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] fs_1.6.1 matrixStats_0.63.0 bitops_1.0-7 lubridate_1.9.2 devtools_2.4.5
[6] webshot_0.5.4 RColorBrewer_1.1-3 httr_1.4.5 doParallel_1.0.17 dynamicTreeCut_1.63-1
[11] gh_1.4.0 numDeriv_2016.8-1.1 profvis_0.3.7 tools_4.3.0 MAGMA.Celltyping_2.0.9
[16] backports_1.4.1 utf8_1.2.3 R6_2.5.1 uwot_0.1.14 lazyeval_0.2.2
[21] withr_2.5.0 urlchecker_1.0.1 gridExtra_2.3 prettyunits_1.1.1 preprocessCore_1.61.0
[26] WGCNA_1.72-1 cli_3.6.1 Biobase_2.59.0 TSP_1.2-4 askpass_1.1
[31] ewceData_1.7.1 Rsamtools_2.15.3 yulab.utils_0.0.6 foreign_0.8-84 R.utils_2.12.2
[36] sessioninfo_1.2.2 plotrix_3.8-2 BSgenome_1.67.4 orthogene_1.5.3 maps_3.4.1
[41] limma_3.55.7 readxl_1.4.2 impute_1.73.0 rstudioapi_0.14 RSQLite_2.3.1
[46] optimParallel_1.0-2 generics_0.1.3 gridGraphics_0.5-1 BiocIO_1.9.2 combinat_0.0-8
[51] dendextend_1.17.1 car_3.1-2 dplyr_1.1.1 homologene_1.4.68.19.3.27 GO.db_3.17.0
[56] Matrix_1.5-3 fansi_1.0.4 S4Vectors_0.37.5 abind_1.4-5 R.methodsS3_1.8.2
[61] lifecycle_1.0.3 scatterplot3d_0.3-43 yaml_2.3.7 carData_3.0-5 SummarizedExperiment_1.29.1
[66] clusterGeneration_1.3.7 BiocFileCache_2.7.2 grid_4.3.0 blob_1.2.4 promises_1.2.0.1
[71] ExperimentHub_2.7.1 crayon_1.5.2 miniUI_0.1.1.1 lattice_0.20-45 GenomicFeatures_1.51.4
[76] KEGGREST_1.39.0 MungeSumstats_1.7.19 pillar_1.9.0 knitr_1.42 GenomicRanges_1.51.4
[81] rjson_0.2.21 boot_1.3-28.1 codetools_0.2-19 fastmatch_1.1-3 glue_1.6.2
[86] ggfun_0.0.9 data.table_1.14.8 remotes_2.4.2 vctrs_0.6.1 png_0.1-8
[91] treeio_1.23.1 cellranger_1.1.0 gtable_0.3.3 assertthat_0.2.1 cachem_1.0.7
[96] xfun_0.38 mime_0.12 coda_0.19-4 survival_3.5-3 gargle_1.3.0
[101] seriation_1.4.2 SingleCellExperiment_1.21.1 RNOmni_1.0.1 iterators_1.0.14 interactiveDisplayBase_1.37.0
[106] ellipsis_0.3.2 nlme_3.1-162 ggtree_3.7.2 EWCE_1.7.4 usethis_2.1.6
[111] bit64_4.0.5 progress_1.2.2 filelock_1.0.2 googleAuthR_2.0.1 GenomeInfoDb_1.35.16
[116] rprojroot_2.0.3 rpart_4.1.19 Hmisc_5.0-1 colorspace_2.1-0 BiocGenerics_0.45.3
[121] DBI_1.1.3 nnet_7.3-18 phangorn_2.11.1 mnormt_2.1.1 tidyselect_1.2.0
[126] processx_3.8.0 bit_4.0.5 compiler_4.3.0 curl_5.0.0 httr2_0.2.2
[131] htmlTable_2.4.1 expm_0.999-7 xml2_1.3.3 ggdendro_0.1.23 DelayedArray_0.25.0
[136] plotly_4.10.1 rtracklayer_1.59.1 checkmate_2.1.0 scales_1.2.1 quadprog_1.5-8
[141] callr_3.7.3 rappdirs_0.3.3 stringr_1.5.0 digest_0.6.31 piggyback_0.1.4
[146] minqa_1.2.5 rmarkdown_2.21 ca_0.71.1 XVector_0.39.0 base64enc_0.1-3
[151] htmltools_0.5.5 pkgconfig_2.0.3 lme4_1.1-32 MatrixGenerics_1.11.1 dbplyr_2.3.2
[156] fastmap_1.1.1 rlang_1.1.0 htmlwidgets_1.6.2 shiny_1.7.4 jsonlite_1.8.4
[161] BiocParallel_1.33.12 R.oo_1.25.0 VariantAnnotation_1.45.1 RCurl_1.98-1.12 magrittr_2.0.3
[166] Formula_1.2-5 GenomeInfoDbData_1.2.10 ggplotify_0.1.0 patchwork_1.1.2 munsell_0.5.0
[171] Rcpp_1.0.10 viridis_0.6.2 ape_5.7-1 babelgene_22.9 stringi_1.7.12
[176] zlibbioc_1.45.0 MASS_7.3-58.3 AnnotationHub_3.7.4 plyr_1.8.8 pkgbuild_1.4.0
[181] parallel_4.3.0 Biostrings_2.67.2 splines_4.3.0 hms_1.1.3 ps_1.7.4
[186] fastcluster_1.2.3 igraph_1.4.2 ggpubr_0.6.0 ggsignif_0.6.4 reshape2_1.4.4
[191] biomaRt_2.55.4 stats4_4.3.0 pkgload_1.3.2 gprofiler2_0.2.1 BiocVersion_3.17.1
[196] XML_3.99-0.14 evaluate_0.20 BiocManager_1.30.20 nloptr_2.0.3 foreach_1.5.2
[201] httpuv_1.6.9 openssl_2.0.6 grr_0.9.5 tidyr_1.3.0 purrr_1.0.1
[206] heatmaply_1.4.2 ggplot2_3.4.2 broom_1.0.4 xtable_1.8-4 restfulr_0.0.15
[211] gitcreds_0.1.2 phytools_1.5-1 tidytree_0.4.2 rstatix_0.7.2 later_1.3.0
[216] viridisLite_0.4.1 googledrive_2.1.0 tibble_3.2.1 aplot_0.1.10 registry_0.5-1
[221] memoise_2.0.1 AnnotationDbi_1.61.2 GenomicAlignments_1.35.1 IRanges_2.33.1 cluster_2.1.4
[226] HGNChelper_0.8.1 timechange_0.2.0 here_1.0.1
bschilder commented
Looks like I actually already accounted for this in the past:
Bizarrely, the FULL_NAME column isn't even consistently generated. So I had to make this conditional:
