• Miscellaneous bugfixes plus a new [0-1] normalization option (see PRs).
• Fixes to noSuggests errors on CRAN
• add rhub workflow file

What's Changed

• Update seqData_wrappers.R by @rarichardson92 in #316
• Fix gtest heatmap incorrectly showing no significance, other issues by @clabornd in #314
• Feature/range scaling norm by @rarichardson92 in #311
• protein_quant: combine different emeta_cols values mapping to a protein by @evanglass in #308
• dont apply imdanova_filter to check for filtered molecules in imd_anova by @clabornd in #319

Full Changelog: v2.4.4...v2.4.5

NOTE: Skipped 2.4.3 due to problems with CRAN submission.

New Features

• Add transcriptomics plots to trelliscope plots by @David-Degnan in #295
• add threshold argument to edata_replace by @clabornd in #306

Bugfixes and Package Misc.

• Fix bad corRes plot when sample names have dashes by @evanglass in #300
• Fix problems with rmd_filter on object with only singletons by @evanglass in #301
• Fix wrong gsub in volcano plot causing duplicated points and bad labels by @clabornd in #305
• fix na-res scatterplot for singleton group datasets [skip ci] by @clabornd in #307
• Move plotly to suggests by @evanglass in #299
• add CRAN badge, add disclaimer about BioConductor repos to README by @clabornd in #303

Full Changelog: v2.4.2...v2.4.4

This is the first stable version on CRAN (resubmit of 2.4.1 to fix some errors in automated checks), go ahead and install.packages("pmartR").
Binaries are also available for certain R versions and operating systems: https://cran.r-project.org/web/packages/pmartR/index.html

Features

• imd_anova now reports the least squares means (aka the estimated marginal means, see the emmeans package) #290 . See the updated "Statistical Analysis with the pmartR Package" article.

Bugfixes

• Fixed imd_anova not handling imbalanced covariates correctly #290
• The proteomics filter now has an order to it: First the degenerate peptides are removed, then proteins without min_num_peps peptides mapping to them are removed. This matters since the removal of degenerate peptides may affect which proteins pass the min_num_peps threshold. #291
• Fixed G-test heatmap plot (option plot_type = 'gheatmap' in plot.statRes) incorrectly ordering axes. #289
• Fixed problem with volcano plots #285
• Various fixes to trelliscope functionality #284
• Fix sample id issue with plot.dimRes #280

Features

• More options for plot.naRes and plot.dimRes

  • Each can color by the grouping factor as well as any columns in f_data
  • plot.naRes can plot count or proportion missing (or non-missing)
  • color_by and shape_by options for plot.dimRes

• Trelliscope plots:

  • Option to filter panels by p-value, see ?trelli_pvalue_filter
  • Small changes to some plots and summary functions

Bugfixes

• Zeros in the data all shared rows with an NA caused pre-flight filtering to remove too many rows #243
• Removed version dependent purrr:: call in pre_flight #246
• Applying two sample filters that removed the same sample erased object #245
• Error in g-test heatmap when there were no significant biomolecules #271
• Make legend order alphabetical on boxplots and other orderable plots #274
• Incorrect titles in some plots, suggesting data was reference or global normalized when it was not #277

• Added RNA-seq data as an omicsData type:

  • Has associated analysis methods DESeq2, limma-VOOM, and edgeR
  • Diagnostic tests and associated plots
  • RNA-seq specific filters totalcountFilt and RNAFilt

• API for trelliscope displays. Create trelliscope displays directly from omicsData objects with a wide choice of plot types. See the vignette on Trelliscope for details.

• Added pvalue adjustment for biomolecules "FDR adjustment". In imd_anova, the arguments pval_adjust_a_multcomp and pval_adjust_g_multcomp now adjust p-values for multiple comparisons within each biomolecule for the anova and g-test. pval_adjust_a_fdr/pval_adjust_g_fdr perform p-value adjustment across all biomolecules.

Incrementing version number to 1.0.0 from 0.10.0