vignettes/other_tools.Rmd
other_tools.Rmd
There are also a lot of useful tools in metid
.
library(metid)
#> ── Attaching packages ─────────────────────────────────────────── metid 1.2.1 ──
#> ✓ tinytools 0.9.1 ✓ massdataset 0.99.1
#> ── Conflicts ────────────────────────────────────────────── metid_conflicts() ──
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#> x massdataset::mz_rt_match() masks tinytools::mz_rt_match()
#> x tinytools::read_mgf() masks metid::read_mgf()
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#> Attaching package: 'metid'
#> The following object is masked _by_ 'package:tinytools':
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#> read_mgf
library(tidyverse)
#> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
#> ✓ ggplot2 3.3.5 ✓ purrr 0.3.4
#> ✓ tibble 3.1.3 ✓ dplyr 1.0.7
#> ✓ tidyr 1.1.3 ✓ stringr 1.4.0
#> ✓ readr 2.0.0 ✓ forcats 0.5.1
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#> x tidyr::extract() masks magrittr::extract()
#> x dplyr::filter() masks massdataset::filter(), stats::filter()
#> x dplyr::lag() masks stats::lag()
#> x purrr::set_names() masks magrittr::set_names()
readMGF
result <- readMGF(file)
readMZXML
result <- readMZXML(file, threads = 3)
readMGF
result <- readMGF(file)
metid
version and logo
metid::metid_logo()
#> Thank you for using metid!
#> Version 1.1.0 (20210702)
#> More information: google tidymass metid.
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sessionInfo()
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
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#> 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] stats graphics grDevices utils datasets methods base
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#> other attached packages:
#> [1] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
#> [5] readr_2.0.0 tidyr_1.1.3 tibble_3.1.3 ggplot2_3.3.5
#> [9] tidyverse_1.3.1 massdataset_0.99.1 magrittr_2.0.1 tinytools_0.9.1
#> [13] metid_1.2.1
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#> [7] GlobalOptions_0.1.2 fs_1.5.0 clue_0.3-59
#> [10] rstudioapi_0.13 mzR_2.26.1 listenv_0.8.0
#> [13] furrr_0.2.3 affyio_1.62.0 lubridate_1.7.10
#> [16] fansi_0.5.0 xml2_1.3.2 codetools_0.2-18
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#> [28] cluster_2.1.2 vsn_3.60.0 png_0.1-7
#> [31] BiocManager_1.30.16 compiler_4.1.0 httr_1.4.2
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#> [37] fastmap_1.1.0 lazyeval_0.2.2 limma_3.48.1
#> [40] cli_3.0.1 htmltools_0.5.2 tools_4.1.0
#> [43] gtable_0.3.0 glue_1.4.2 affy_1.70.0
#> [46] Rcpp_1.0.7 MALDIquant_1.20 Biobase_2.52.0
#> [49] cellranger_1.1.0 jquerylib_0.1.4 pkgdown_2.0.1
#> [52] vctrs_0.3.8 preprocessCore_1.54.0 iterators_1.0.13
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#> [61] XML_3.99-0.6 future_1.21.0 zlibbioc_1.38.0
#> [64] MASS_7.3-54 scales_1.1.1 MSnbase_2.18.0
#> [67] ragg_1.1.3 pcaMethods_1.84.0 hms_1.1.0
#> [70] ProtGenerics_1.24.0 parallel_4.1.0 RColorBrewer_1.1-2
#> [73] ComplexHeatmap_2.8.0 yaml_2.2.1 memoise_2.0.0
#> [76] pbapply_1.4-3 sass_0.4.0 stringi_1.7.3
#> [79] S4Vectors_0.30.0 desc_1.3.0 foreach_1.5.1
#> [82] BiocGenerics_0.38.0 zip_2.2.0 BiocParallel_1.26.1
#> [85] shape_1.4.6 rlang_0.4.11 pkgconfig_2.0.3
#> [88] systemfonts_1.0.2 matrixStats_0.60.0 mzID_1.30.0
#> [91] evaluate_0.14 lattice_0.20-44 htmlwidgets_1.5.3
#> [94] tidyselect_1.1.1 ggsci_2.9 parallelly_1.27.0
#> [97] plyr_1.8.6 R6_2.5.0 IRanges_2.26.0
#> [100] generics_0.1.0 DBI_1.1.1 withr_2.4.2
#> [103] haven_2.4.1 pillar_1.6.2 MsCoreUtils_1.4.0
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#> [109] plotly_4.9.4.1 tzdb_0.1.2 rmarkdown_2.9
#> [112] GetoptLong_1.0.5 grid_4.1.0 readxl_1.3.1
#> [115] data.table_1.14.0 reprex_2.0.0 digest_0.6.27
#> [118] gridGraphics_0.5-1 textshaping_0.3.6 stats4_4.1.0
#> [121] munsell_0.5.0 ggplotify_0.0.8 viridisLite_0.4.0
#> [124] bslib_0.3.1