Function 'GetGroupNames' not found

MetaboAnalyst
1

Hi,
I’m using the package with no problems with several functions working. However it seems that there is some problem with ‘GetGroupNames’ function.
See:

GetGroupNames
Error: object ‘GetGroupNames’ not found

trying to run:

mSet<-GetGroupNames(mSet, “”)
Error in GetGroupNames(mSet, “”) :
could not find function “GetGroupNames”

sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] Rserve_1.8-10 MetaboAnalystR_3.0.3

loaded via a namespace (and not attached):
[1] fastmatch_1.1-3 sn_2.1.0 plyr_1.8.8 igraph_1.3.5 splines_4.2.0
[6] BiocParallel_1.32.1 listenv_0.8.0 ggplot2_3.4.0 qqconf_1.3.0 TH.data_1.1-1
[11] digest_0.6.30 foreach_1.5.2 htmltools_0.5.3 fansi_1.0.3 magrittr_2.0.3
[16] memoise_2.0.1 cluster_2.1.4 doParallel_1.0.17 limma_3.54.0 recipes_1.0.3
[21] globals_0.16.1 gower_1.0.0 sandwich_3.0-2 hardhat_1.2.0 timechange_0.1.1
[26] siggenes_1.72.0 prettyunits_1.1.1 colorspace_2.0-3 blob_1.2.3 rbibutils_2.2.10
[31] dplyr_1.0.10 crayon_1.5.2 jsonlite_1.8.3 graph_1.76.0 impute_1.72.1
[36] survival_3.4-0 zoo_1.8-11 iterators_1.0.14 glue_1.6.2 gtable_0.3.1
[41] ipred_0.9-13 zlibbioc_1.44.0 future.apply_1.10.0 BiocGenerics_0.44.0 scales_1.2.1
[46] vsn_3.66.0 mvtnorm_1.1-3 DBI_1.1.3 edgeR_3.40.0 Rcpp_1.0.9
[51] metap_1.8 plotrix_3.8-2 mzR_2.32.0 progress_1.2.2 clue_0.3-62
[56] bit_4.0.4 preprocessCore_1.60.0 stats4_4.2.0 MsCoreUtils_1.10.0 lava_1.7.0
[61] prodlim_2019.11.13 httr_1.4.4 fgsea_1.24.0 gplots_3.1.3 RColorBrewer_1.1-3
[66] TFisher_0.2.0 ellipsis_0.3.2 pkgconfig_2.0.3 reshape_0.8.9 XML_3.99-0.12
[71] nnet_7.3-18 locfit_1.5-9.6 utf8_1.2.2 caret_6.0-93 tidyselect_1.2.0
[76] rlang_1.0.6 reshape2_1.4.4 munsell_0.5.0 tools_4.2.0 cachem_1.0.6
[81] cli_3.4.1 generics_0.1.3 RSQLite_2.2.18 pls_2.8-1 mathjaxr_1.6-0
[86] stringr_1.4.1 fastmap_1.1.0 mzID_1.36.0 ModelMetrics_1.2.2.2 bit64_4.0.5
[91] caTools_1.18.2 crmn_0.0.21 scrime_1.3.5 purrr_0.3.5 ncdf4_1.19
[96] RBGL_1.74.0 future_1.29.0 nlme_3.1-160 compiler_4.2.0 rstudioapi_0.14
[101] affyio_1.68.0 tibble_3.1.8 stringi_1.7.8 MSnbase_2.24.0 lattice_0.20-45
[106] ProtGenerics_1.30.0 Matrix_1.5-3 multtest_2.54.0 vctrs_0.5.0 mutoss_0.1-12
[111] pillar_1.8.1 lifecycle_1.0.3 BiocManager_1.30.19 Rdpack_2.4 MALDIquant_1.22
[116] data.table_1.14.4 cowplot_1.1.1 bitops_1.0-7 R6_2.5.1 pcaMethods_1.90.0
[121] affy_1.76.0 KernSmooth_2.23-20 IRanges_2.32.0 parallelly_1.32.1 codetools_0.2-18
[126] MASS_7.3-58.1 gtools_3.9.3 withr_2.5.0 mnormt_2.1.1 multcomp_1.4-20
[131] S4Vectors_0.36.0 parallel_4.2.0 hms_1.1.2 grid_4.2.0 rpart_4.1.19
[136] timeDate_4021.106 tidyr_1.2.1 class_7.3-20 Cairo_1.6-0 pROC_1.18.0
[141] rsm_2.10.3 numDeriv_2016.8-1.1 Biobase_2.58.0 lubridate_1.9.0

2

This function is for our web application. If you need to access the group names in R, you can use basic R functions, something like

> mSetObj$dataSet$cls

3

Thanks, I was trying to reproduce the codes for removing a specific group. But it seems that the commands provided by the website are not enough.
So I did a little routine for removing the QC group. I share it here to help anyone who wants to do the same operation locally.

remove.group ← “QC”

data ← mSet$dataSet$filt;
cls ← mSet$dataSet$filt.cls;

samp.grp.map ← data.frame(samples = rownames(data), groups = cls)

idx.remove ← which(samp.grp.map$groups == remove.group)

message("Remove index = “, paste(shQuote(idx.remove,
type=“sh”), collapse=”, "), “\nSamples = " ,
paste(shQuote(samp.grp.map$samples[idx.remove],
type=“sh”), collapse=”, "))

samp.grp.map ← samp.grp.map %>% filter(groups != remove.group) %>% droplevels()

update

mSet$dataSet$edit ← data[samp.grp.map$samples,];
mSet$dataSet$edit.cls ← samp.grp.map$groups;

message("New groups = “, paste(shQuote(levels(mSet$dataSet$edit.cls),
type=“sh”), collapse=”, "))