pmartR / pmartR

The pmartR R package provides functionality for quality control, normalization, exploratory data analysis, and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data.

https://pmartr.github.io/pmartR/

pmartR/pmartR Issues

Error running spans_procedure
Updated 16 days ago3
IMD-Anova filter does not carry through protein roll-up, which sometimes prevents protein-level analyses using imd_anova
Closed 21 days ago2
protein_quant() -- Argument emeta_cols doesn't seem to keep the columns specified?
Closed 21 days ago3
G-test heatmap sometimes fails to mark significant cells
Closed a month ago4
cov_type = 'numeric' doesn't work?
Updated 2 months ago
On the off chance someone doesn't filter -- non-explicit error for protein_quant
Updated 2 months ago2
Developer: trim build/check time
Closed 2 months ago
Allow pmartR to accept e_meta with duplicate edata_cname and emeta_cname pairings
Updated 3 months ago1
dimRes object does not inherit data.frame?
Updated 3 months ago
Singleton groups cause an error in plot.nares
Closed 4 months ago
add a thresholding option to edata_replace, so that everything below a specified threshold is considered NA
Closed 4 months ago1
Easy Fix: Volcano plot mislabeling points
Closed 4 months ago1
Move plotly to Suggests
Closed 5 months ago
rmd_filter on object with only singleton groups fails
Closed 5 months ago1
Trelliscope Functions: Fixes and new Features
Closed 5 months ago
suggestion to replace vignettes: articles
Closed 6 months ago1
Prep flags check names
Closed 9 months ago
Plotting dimres object fails if fdata_cname is not "SampleID"
Closed 9 months ago
Error to install on windows
Closed 10 months ago3
Track down and destroy warnings/notes in R-CMD-Check [CRAN]
Closed 10 months ago
Use -id_col instead of -1
Closed 10 months ago
minor vignette updates
Closed a year ago1
plot.omicsData plot title incorrect with pre-normalized object
Closed a year ago1
plot of omicsData object always has "Reference Standardized" in the title
Closed a year ago1
Error in fold change computation when control group name is a substring of the test group name
Closed a year ago2
combine_lipids errors our when duplicate e_meta names are present
Closed a year ago3
Plotting of g-test stats results gives wrong values
Updated a year ago
More options for plot.naRes
Closed a year ago3
Error in nonmissing_per_group count assignment when edata and fdata sample ordering differs
Closed a year ago3
Possible memory issue with imd_anova()
Closed a year ago2
imd-anova incorrect p-values
Closed a year ago
Error in rmd plotting from pair_id peptides from plot_fn.R
Closed a year ago1
Two sample filters with the same sample erase the object
Closed a year ago2
emeta_cname shows up in object
Closed a year ago4
summary.customFilt cant find variable when using "keep" mode
Closed 2 years ago1
add automatic filter at omicData object creation to remove any rows of e_data that are all missing
Updated 2 years ago
plot.rmdFilt does not currently have capability to "order_by"
Closed 2 years ago1
plot.rmdFilt includes a legend entry related to pairing even when data object is not paired
Closed 2 years ago1
Group counts not always returned by imd_anova()
Closed 2 years ago1
combine_lipidData duplicates f_data
Closed 2 years ago3
Extra check for pair_id + pair_group
Closed 2 years ago1
check in pre-flight causing protein rollup to crash
Closed 2 years ago1
imdanova throws error if no imdanova filter has been run
Closed 2 years ago2
applyFilt.customFilter complains if you've already applied a custom filter and this is silly
Closed 2 years ago1
dim_reduction() function needs minor fix line 76
Closed 2 years ago1
imdCov branch: for anova_filter and gtest_filter, default comparisons = NULL
Closed 2 years ago1
Columns names change due to the check.names argument in the data.frame function
Closed 2 years ago1
Numeric arguments incorrectly accept character string inputs
Closed 2 years ago1
plot.imdanovaFilt fails when specifying both min_nonmiss options
Closed 2 years ago2
pmartR v0.10.0 imd_test issue
Closed 2 years ago1