Closed adannasusan closed 1 year ago
Hey, I see you have quite an old version of MSS installed (1.4.5) the current release is v1.8.0, can you please update to at least this version and see if the error persists? Also if it does please attach a dataset that will give the same error so I can work to debug it (the save ldsc option works on our sample data with v1.8.0). Cheers, Alan.
Closing because of inactivity, feel free to reopen if this doesn't clear things up
1. Bug description
Whenever I use save_format='LDSC' in format_sumstats(), it always returns an error.
Console output
Paste console output here (e.g. from R/python/command line)
Error in MungeSumstats::format_sumstats(path = file, ref_genome = "GRCh37", : unused argument (save_format = "LDSC")
Expected behaviour
I expected it to save my sumstats in Ldsc format.
2. Reproducible example
Code
(Please add the steps to reproduce the bug here. See here for an intro to making a reproducible example (i.e. reprex) and why they're important! This will help us to help you much faster.)
Paste utils::sessionInfo() output
R version 4.2.1 (2022-06-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS/LAPACK: /apps/eb/OpenBLAS/0.3.12-GCC-10.2.0/lib/libopenblas_zenp-r0.3.12.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] MungeSumstats_1.4.5 rio_0.5.29 forcats_0.5.1
[4] stringr_1.5.0 dplyr_1.1.2 purrr_1.0.1
[7] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[10] ggplot2_3.4.2 tidyverse_1.3.2
loaded via a namespace (and not attached): [1] bitops_1.0-7 matrixStats_0.62.0
[3] fs_1.5.2 bit64_4.0.5
[5] lubridate_1.8.0 filelock_1.0.2
[7] progress_1.2.2 httr_1.4.6
[9] googleAuthR_2.0.1 GenomeInfoDb_1.32.2
[11] tools_4.2.1 backports_1.4.1
[13] utf8_1.2.2 R6_2.5.1
[15] DBI_1.1.3 BiocGenerics_0.42.0
[17] colorspace_2.0-3 withr_2.5.0
[19] prettyunits_1.1.1 tidyselect_1.2.0
[21] bit_4.0.5 curl_5.0.1
[23] compiler_4.2.1 cli_3.6.1
[25] rvest_1.0.3 Biobase_2.56.0
[27] xml2_1.3.3 DelayedArray_0.22.0
[29] rtracklayer_1.56.1 scales_1.2.1
[31] rappdirs_0.3.3 digest_0.6.31
[33] Rsamtools_2.12.0 foreign_0.8-82
[35] R.utils_2.12.0 XVector_0.36.0
[37] pkgconfig_2.0.3 MatrixGenerics_1.8.1
[39] fastmap_1.1.0 dbplyr_2.2.1
[41] BSgenome_1.64.0 rlang_1.1.1
[43] readxl_1.4.0 RSQLite_2.2.15
[45] BiocIO_1.6.0 generics_0.1.3
[47] jsonlite_1.8.5 BiocParallel_1.30.3
[49] zip_2.2.0 R.oo_1.25.0
[51] googlesheets4_1.0.0 VariantAnnotation_1.42.1
[53] RCurl_1.98-1.7 magrittr_2.0.3
[55] GenomeInfoDbData_1.2.8 Matrix_1.4-1
[57] Rcpp_1.0.10 munsell_0.5.0
[59] S4Vectors_0.34.0 fansi_1.0.3
[61] lifecycle_1.0.3 R.methodsS3_1.8.2
[63] stringi_1.7.12 yaml_2.3.7
[65] SummarizedExperiment_1.26.1 zlibbioc_1.42.0
[67] BiocFileCache_2.4.0 blob_1.2.3
[69] grid_4.2.1 parallel_4.2.1
[71] crayon_1.5.2 lattice_0.20-45
[73] Biostrings_2.64.0 haven_2.5.0
[75] GenomicFeatures_1.48.3 KEGGREST_1.36.3
[77] hms_1.1.3 pillar_1.9.0
[79] GenomicRanges_1.48.0 rjson_0.2.21
[81] biomaRt_2.52.0 codetools_0.2-18
[83] stats4_4.2.1 reprex_2.0.1
[85] XML_3.99-0.10 glue_1.6.2
[87] data.table_1.14.8 modelr_0.1.8
[89] png_0.1-7 vctrs_0.6.2
[91] tzdb_0.3.0 cellranger_1.1.0
[93] gtable_0.3.3 assertthat_0.2.1
[95] cachem_1.0.6 openxlsx_4.2.5
[97] broom_1.0.0 restfulr_0.0.15
[99] googledrive_2.0.0 gargle_1.2.0
[101] AnnotationDbi_1.58.0 memoise_2.0.1
[103] GenomicAlignments_1.32.0 IRanges_2.30.0