benjaminjack / parsemsf Goto Github PK
View Code? Open in Web Editor NEWAn R package for parsing Thermo MSF mass spectrometry files
An R package for parsing Thermo MSF mass spectrometry files
Hello,
Thank you for developing so nice software!
I just went to go through the demo data.
Thank you in advance for your great help!
Best,
Yue
> library(parsemsf)
> area_table <- make_area_table(parsemsf_example("test_db.msf"))
Error in UseMethod("select_") : no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
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 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] parsemsf_0.1.1 dplyr_1.0.2 AnnotationHub_2.18.0 BiocFileCache_1.10.2 dbplyr_2.0.0 ensembldb_2.10.2 AnnotationFilter_1.10.0
[8] GenomicFeatures_1.38.2 AnnotationDbi_1.48.0 Biobase_2.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 IRanges_2.20.2 S4Vectors_0.24.4
[15] BiocGenerics_0.32.0 limma_3.42.2
loaded via a namespace (and not attached):
[1] colorspace_2.0-0 ellipsis_0.3.1 htmlTable_2.1.0 XVector_0.26.0 base64enc_0.1-3
[6] rstudioapi_0.13 bit64_4.0.5 interactiveDisplayBase_1.24.0 splines_3.6.3 geneplotter_1.64.0
[11] knitr_1.30 Formula_1.2-4 Rsamtools_2.2.3 annotate_1.64.0 cluster_2.1.0
[16] png_0.1-7 shiny_1.5.0 BiocManager_1.30.10 compiler_3.6.3 httr_1.4.2
[21] backports_1.2.0 assertthat_0.2.1 Matrix_1.2-18 fastmap_1.0.1 lazyeval_0.2.2
[26] later_1.1.0.1 htmltools_0.5.0 prettyunits_1.1.1 tools_3.6.3 gtable_0.3.0
[31] glue_1.4.2 GenomeInfoDbData_1.2.2 rappdirs_0.3.1 Rcpp_1.0.5 vctrs_0.3.5
[36] Biostrings_2.54.0 rtracklayer_1.46.0 xfun_0.19 stringr_1.4.0 mime_0.9
[41] lifecycle_0.2.0 XML_3.99-0.3 zlibbioc_1.32.0 scales_1.1.1 hms_0.5.3
[46] promises_1.1.1 ProtGenerics_1.18.0 SummarizedExperiment_1.16.1 RColorBrewer_1.1-2 yaml_2.2.1
[51] curl_4.3 memoise_1.1.0 gridExtra_2.3 ggplot2_3.3.2 biomaRt_2.42.1
[56] rpart_4.1-15 latticeExtra_0.6-29 stringi_1.5.3 RSQLite_2.2.1 BiocVersion_3.10.1
[61] genefilter_1.68.0 checkmate_2.0.0 BiocParallel_1.20.1 rlang_0.4.9 pkgconfig_2.0.3
[66] matrixStats_0.57.0 bitops_1.0-6 lattice_0.20-41 purrr_0.3.4 GenomicAlignments_1.22.1
[71] htmlwidgets_1.5.2 bit_4.0.4 tidyselect_1.1.0 magrittr_2.0.1 DESeq2_1.26.0
[76] R6_2.5.0 generics_0.1.0 Hmisc_4.4-2 DelayedArray_0.12.3 DBI_1.1.0
[81] pillar_1.4.7 foreign_0.8-76 survival_3.2-7 RCurl_1.98-1.2 nnet_7.3-14
[86] tibble_3.0.4 crayon_1.3.4 jpeg_0.1-8.1 progress_1.2.2 locfit_1.5-9.4
[91] grid_3.6.3 data.table_1.13.2 blob_1.2.1 digest_0.6.27 xtable_1.8-4
[96] tidyr_1.1.2 httpuv_1.5.4 openssl_1.4.3 munsell_0.5.0
> make_area_table(parsemsf_example("test_db.msf"))
Error in UseMethod("select_") :
no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
Calls: make_area_table ... _fseq -> freduce -> withVisible -> <Anonymous> -> select_
Execution halted
I'd recommend updating to use tidyeval, since these methods are likely to be removed in the next version of dbplyr.
I have installed parsemsf package to the Rstudio environment. I have my msf files in working directory. I am using the following code.
library(parsemsf) sample4_2=make_area_table("ESC-HF-S10-10-1-Siddharth-230118.msf", min_conf = "High", prot_regex = "^>([a-zA-Z0-9._]+)\\b", collapse = TRUE)
The code is giving me following error
Error in enc2utf8(col_names(col_labels, sep = sep)) :
argument is not a character vector
Kindly help
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