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Home Page: http://EMSL-Computing.github.io/ftmsRanalysis
License: Other
I'm trying to run the uniqueness_gtest function in order to plot a van Krevelen diagram showing compounds unique to each group. I have 3 replicates in each group. Even expanding the significance threshold to 0.15, I'm not getting anything as significant, across nearly 20 comparisons. I've gone through and looked and there are some instances where I have 3 replicates seen in one group and only 1 in the other - seems like this should pop out? Looking at NOSC comparisons, there are obvious differences, so it's weird that nothing is showing up in the van Krevelen.
peak_data = as.peakData(e_data = edata, f_data = fdata, e_meta = emeta, edata_cname = "Mass", fdata_cname = "SampleID",
mass_cname = "Mass", c_cname = "C", h_cname = "H", o_cname = "O", n_cname = "N", s_cname = "S", p_cname = "P", isotopic_cname = "C13", isotopic_notation = "1")
Error in .as.peakData(e_data, f_data, e_meta, edata_cname, fdata_cname, :
The 'edata_cname' identifier is non-unique.
package ‘glue’ successfully unpacked and MD5 sums checked
Error: Failed to install 'ftmsRanalysis' from GitHub:
(converted from warning) cannot remove prior installation of package ‘glue’
Any suggestions? Thanks!
Hello! I have used your excellent package for exploring my FT-ICR-MS data sets without incident until I inadvertently tried assembling a new peakData object with tibbles instead of strictly using data frames. These were products of some preliminary filtering with dplyr functions and readr::read_table. Then as.peakData seemed happy to accept them as inputs and construct a peakData object. I ran compound_calcs and got an error reading "Error in [<-.data.frame
(*tmp*
, ai_ids, value = 0) : new columns would leave holes after existing columns". Modifying all the as.peakData inputs with as.data.frame() and rebuilding the peakData object worked fine, but it took a little while to figure out why it suddenly seemed like compound_calcs wasn't working. Thought you might be interested in case anyone else runs into this! Here's a quick console screenshot in case that helps illustrate.
In running the vignette ftmsRanalysis.Rmd
I got the following error at line 301
byGroup <- divideByGroupComparisons(peakObj,
comparisons = "all")[[1]]$value
Loading required package: datadr
there is no package called ‘datadr’Error in kvPair(key, val) : could not find function "kvPair"
However, when I search for datadr
https://cran.r-project.org/web/packages/datadr/index.html
Package ‘datadr’ was removed from the CRAN repository.
Formerly available versions can be obtained from the archive.
Archived on 2020-01-02 as nothing now depends on it.
The most recent check results can be obtained from the check results archive.
However even in the archive the package is not available.
If I try to just knit the whole file I get hung at the same point with the attached error
![ftmsRanalysis](https://user-images.githubusercontent.com/4509174/97483485-da341080-192d-11eb-8de6-58e729238025.png)
applyFilt tries to subset the mass filter based on edata_cname, which will not always be the same as mass_cname:
Line 137 in 6df6a14
Making applyFilt use mass_cname doesn't work either because summary.massFilt and plot.massFilt both have hard-coded references to the "Mass" column:
Line 137 in 6df6a14
ftmsRanalysis/R/filter_summary_methods.R
Line 71 in 6df6a14
See #17
Warning in install.packages :
package ‘ftmsRanalysis’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
We're removing these packages as dependencies. Certain functions can just be chopped entirely it looks like, but others, such as ones that perform uniqueness_gtest
need to be updated.
See branch remove_ddr
In the constructor for peakData objects, we currently have one argument to specify the column name for each of C, H, N, O, S, P.
https://github.com/EMSL-Computing/ftmsRanalysis/blob/master/R/as.ftmsData.R
We want to be able to do this for many atoms, such as listed in atoms_order
in coreMS. Probably what this will look like is passing it a named vector or list like: list( = , = , = ), which defaults to something like: list("C" = "C", "H" = "H", "N" = "N", "O" = "O", "S" = "S", "P" = "P") , but the user could specify, for instance list("C" = "C", "H" = "H", "Bi" = "Bi_column")
This is going to necessitate a lot of changes:
Hi, install via devtools::install_github("EMSL-Computing/ftmsRanalysis") reported cannot open URL 'https://api.github.com/repos/EMSL-Computing/ftmsRanalysis/tarball/HEAD'.
Installing the file "EMSL-Computing-ftmsRanalysis-6df6a14.tar.gz" from a local folder also failed with a "package installation had non zero exit status"
The package Description file indicates R version > 3.4.0 will work. I'm using 4.2. Any suggestions? Thank you,
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
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
attached base packages:
[1] stats graphics grDevices datasets utils methods
[7] base
other attached packages:
[1] devtools_2.4.3 usethis_2.1.6
loaded via a namespace (and not attached):
[1] magrittr_2.0.3 pkgload_1.2.4 R6_2.5.1
[4] rlang_1.0.2 fastmap_1.1.0 tools_4.2.0
[7] pkgbuild_1.3.1 sessioninfo_1.2.2 cli_3.3.0
[10] withr_2.5.0 ellipsis_0.3.2 remotes_2.4.2
[13] rprojroot_2.0.3 lifecycle_1.0.1 crayon_1.5.1
[16] brio_1.1.3 processx_3.6.1 purrr_0.3.4
[19] callr_3.7.0 fs_1.5.2 ps_1.7.1
[22] curl_4.3.2 testthat_3.1.4 memoise_2.0.1
[25] glue_1.6.2 cachem_1.0.6 compiler_4.2.0
[28] desc_1.4.1 prettyunits_1.1.1 renv_0.15.5
The below fails
library(ftmsRanalysis)
data("ftms12T_edata")
data("ftms12T_fdata")
data("ftms12T_emeta")
edata <- ftms12T_edata
edata[edata == 0] <- NA
peakObj <- as.peakData(edata, ftms12T_fdata, ftms12T_emeta,
edata_cname="Mass", fdata_cname="SampleID",
mass_cname="Mass", c_cname="C", h_cname="H",
o_cname="O", n_cname="N", s_cname="S",
p_cname="P", isotopic_cname = "C13",
isotopic_notation = "1", check_rows = T)
Error in if (any(molfilt$Num_Observations == 0)) res <- applyFilt(molfilt, :
missing value where TRUE/FALSE needed
The error appears to begin with the molecule_filter() call:
Line 291 in 13634ad
which then calls n_present(), which calls rowSums() on an object with NA's producing NA's in the output:
ftmsRanalysis/R/group_summary_functions.R
Line 12 in 13634ad
Then the any() call in the error message returns an NA since molfilt$Num_Observations contains NA's.
I can't find any way to customize the final graph in https://emsl-computing.github.io/ftmsRanalysis/articles/ftmsRanalysis.html.
Observed in both is sometimes not useful to see and the compound classes get in the way.
The molecular formula format in the e_data and mc_compounds data from MetaCyc is not consistent, one is CHNOSP, and the other is CHONSP.
Inner_joining these two data by formula for mapping peak FT-MS data to compounds may be problematic.
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