Changelog

Source: NEWS.md

msDiaLogue 0.0.6

• Analysis:
  • Separate all options into individual functions analyze.*().
  • Addanalyze.plsda().
  • Rewrite analyze.pca() and analyze.plsda() to improve clarity.
• Visualization:
  • Separate all options into individual functions visualize.*().
  • Add visualize.rank().
  • Rename visualize.ind() to visualize.score() to ensure compatibility with PLS-DA and any other future analyses that include scores.
  • Rename visualize.var() to visualize.loading() to ensure compatibility with PLS-DA and any other future analyses that include loadings.
  • Add visualize.vip().
• Vignette:
  • Separate usage template into individual modules.
  • Add an FAQ section.
• Add NEWS.

msDiaLogue 0.0.5

• preProcessFiltering(): Intended for internal use only.

• preprocessing_scaffold():

  • Make it compatible with the scaffold files containing GO information.
  • Add arguments zeroNA and oneNA to replace 0s and 1s with NAs.
  • Make it compatible with data without AlternateID.
    
    

• transform(): Add root transformation.

• normalize():

  • Add argument plot.
  • Add scaling and centering.
    
    

• impute.*():

  • Add the “R.Condition” and “R.Replicate” columns to the shadow matrix.
  • Use NA to represent missing values in both the pre- and post-imputation data.
    
    

• analyze():

  • Make it capable of performing multiple comparisons and reconstruct the result structure.
  • Add Wilcoxon test (method = "wilcox-test").
  • Add PCA (method = "PCA"; seperate PCA into analyze and visualize).
  • Add argument adjust.method.
    
    

• visualize():

  • MA: Change the labels for the x and y axes; remove the title; change ‘significant’ in the legend to ‘regulation’; make it compatible with the whole result list.
  • normalize: Remove the title.
  • test: Make it compatible with the whole result list.
  • Venn: Add the argument saveVenn to save the data in the Venn plot.
  • volcano: Make it compatible with the whole result list.
  • PCA_ind and PCA_biplot: Remove the ‘a’ marker from the scatter in the legend.
    
    

• Other:

  • dataMissing(): Add arguments sort_miss, show_pct_legend, and show_pct_col.
  • pullProteinPath(): Add arguments listName, regexName, and by.
    
    

• vignette:

  • Change the note block border color to a paler red.
  • Add the instructions for addressing installation issues.
  • Add instructions for Bioconductor package installation.
  • Add cust_vis.
  • Update the example data.

msDiaLogue 0.0.4

• For imputation, separate all options into individual functions, add impute.mice_cart(), impute.mice_norm(), impute.pca_bayes() and impute.pca_prob().

• Use autoglobal.

• preprocessing(): add the hist for raw data; fix colnames.

• filterOutIN(): fix regex.

• visualize(): fix the point shape in the legend (ggrepel).

• analyze(): fix the factor level consistent with the input.

• Rewrite trimFASTA().

• Drop R.FileName in all functions.

• Add preprocessing_scaffold().

• Revise filterProtein() to make it compatible with Scaffold.

• Add note css.

msDiaLogue 0.0.3

• For impute(), add options for "knn", "seq-knn", "trunc-knn" and "nuc-norm".

• Add filterProtein().

• For visualize(), add support for "Upset".

msDiaLogue 0.0.2

• Add moderated t-test in analyze().

• dataMissing(): Calculate the count of missing data.

• Revise normalize() to ensure compatibility with missing values (NAs) during the normalization process before proceeding with imputation.

• Revise summarize() to create a comprehensive descriptive summary.

• Rewrite visualize() and add some graphType related to PCA.

• Update and smooth the entire package.

• Build the website.

msDiaLogue 0.0.1

• First release of the package.