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Update History

updates.Rmd

Versioning follows a semantic scheme with a brief accounting of the major updates and bug-fixes listed here. For quick reference:

  • x.x.N - minor updates or bug fixes

  • x.N.x - introduction of new features or improvements that should not break existing implementations

  • N.x.x - major updates or changes that would break backward compatibility

Version: 1.8.x

1.8.5 - 2024.12.18

  • Minor fix to normalize() [thanks: github.com/tywang-tw] where after limma NA are reintroduced into the quantitative data table compromising later data exports.

1.8.4 - 2024.10.14

  • Minor fix to merge() |> export_quant() [thanks: github.com/tywang-tw] where the quantitative source ‘selected’ was not recognized. This has been addressed, however, it is un-advised to normalize() prior to merge() as the possibility exists to have different normalization methods used between sets and major quantitative offsets, that normalization is intended to address, persist or become exaggerated, increasing the probability of false positives in downstream analyses.

1.8.3 - 2024.09.24

  • Implemented additional columns on to calculate the fraction imputed per sample when exporting to a flat table [thanks: github.com/tywang-tw].
  • Bug fix on peptide-to-protein collapse in some cases resulting in expanded sample sizes due to mismatch on table merge.
  • Bug fix to account for enrichment estimates when protein log2 fold change values are significantly skewed.

1.8.2 - 2024.08.02

  • Updated the volcano plot to include auto-generated titles, classic theme, plotting only y=p-value with either p-value or adj-p-value significance cutoffs and removing values with p-value==1.

1.8.1 - 2024.07.30

  • Added Fisher’s Exact Test (Over-Representation Analysis) to enrichment() function.
  • Added the ability to automate both expression() and enrichment() functions with updated .terms parameter
  • Added the analyze_expressions() and analyze_enrichments() to compliment the automation by saving out plots and tables for each expression and enrichment test.

Version: 1.7.x

1.7.4 - 2024.06.04

  • Bug fix missing package reference in limma expression analysis

1.7.3 - 2024.03.12

  • fixed issue with importing FragPipe tsv files, seems to be an issue with the vroom package. Modified to use the readr package for data importing.
  • modified the export_quant() function to allow exporting proteins with NAs for all samples
  • changed subset() to be an S3 function

1.7.2 - 2024.01.24

  • fixed and issue with plot_counts and plot_variation_cv failed to account for sample sets larger than 16 when providing a color palette

1.7.1 - 2024.01.23

  • new release to add DOI from Zenodo

1.7.0 - 2023.12.13

  • add the ability to export the proteins specific to a given Venn intersection extracting
  • minor improvements on the export_analysis function to clarify column headers

Version: 1.6.x

1.6.1 - 2023.11.29

  • fixed some minor issues
  • implemented the request from issue#9 adding the quantitative values to the export_analysis() function
  • implemented the request from issue#12 allowing for the iterative evaluation of multiple comparisons for the expression() and enrichment() functions

1.6.0 - 2023.11.09

  • fixed an issue with improper missing value accounting when implementing expression tests [thanks: github.com/rzieg]

Version: 1.5.x

1.5.10 - 2023.11.03

  • addressed issues#9 & #10 to better handle as.data.frame [thanks: github.com/tywang-tw]

1.5.9 - 2023.10.30

  • addressed issue#8 to better handle the text of custom functions [thanks: github.com/michwij]

1.5.8 - 2023.10.10

  • addressed issue#5 with the default MaxQuant protein import definition [thanks: tar226-at-cornell.edu]

1.5.7 - 2023.09.21

  • addressed issue#4 with enrichment() taking long for complex annotations, implemented parallel::mclapply [thanks: github.com/eschen42]
  • created a export_config() function to assist in custom import definitions [thanks: github.com/eschen42]

1.5.6 - 2023.09.07

  • addressed issue#3: t.test on expression diff fails on no variance data
  • fixed issue with reporting imputation in object details and record of operations

1.5.5 - 2023.08.24

  • fixed deprecated issue in subset (tidyr::pivot_wider)
  • fixed issue with use R v4+ pipe operator
  • other minor improvements

1.5.4 - 2023.08.16

  • added support for selecting fgsea scoreType(“std”, “pos”, “neg”) [thanks: github.com/tywang-tw]

1.5.3 - 2023.07.30

  • added theme color support for plotting 16+ sample groups

1.5.2 - 2023.06.29

  • bug fix in limma expression differences (name ordering only effecting data with 3+ sample groups) [thanks: github.com/tywang-tw]

1.5.1 - 2023.06.09

  • updated plot_counts(), added show_replicates = T/F

1.5.0 - 2023.05.23

  • refactored impute() to allow for user defined matrix based functions
  • refactored reassign() to use expressive comparisons
  • added export_compexp() to export the data under the two-expression plot
  • updated plot_variation_cv() to better label y-axis
  • modified summary() for peptides using simpler accounting
  • bugfix on import() allowing > 0 annotation columns
  • bugfix in summary() with table merging
  • bugfix in annotate() with leftover dplyr groups

Version: 1.4.x

1.4.2 - 2023.04.03

  • updated color theme to maximize contrasts in order
  • updated plot_quantrank() to further fade background points when using a display_subset

1.4.1 - 2023.03.28

  • migrated from dplyr deprecated across() to group_by_at()
  • minor bugfix on accounting by non-protein based values

1.4.0 - 2023.03.27

  • added the S3Method as.data.frame()

Version: 1.3.x

1.3.1 - 2023.03.20

  • minor code updates to improve conciseness
  • added display_subset to plot_quantrank() to highlight user selected proteins/peptides amoung the whole dynamic range

1.3.0 - 2023.03.13

  • addressed multiple charge precursor in peptide quant files
  • added FragPipe to the available imports
  • exposed adjust.p.value method selection in expression()
  • exposed the user defined import option
  • fixed a labeling error in plot_pca()
  • modified the method for pivoting columns-to-rows in import files

Version: 1.2.x

1.2.6 - 2023.03.01

  • added clarity around normalize(), impute(), collapse()
  • implemented parallel processing for ‘randomforest’ and ‘svm’ in normalize()
  • added a vignette on protein inferencing using collapse()
  • fixed a bug in peptide importing that removed homologous peptide accounting

1.2.5 - 2023.02.13

  • fixed an issue with MBR accounting

1.2.4 - 2023.02.03

  • added support for mzTab v1.0.0, exporting table for counts analysis

Version: 1.1.x

1.1.2 - 2023.01.23

  • refactored the import function to allow both wide and long format data in a configuration file, eliminating the hard coded import functions for ProteomeDiscoverer and MaxQuant

Version: 1.0.x

1.0.4 - 2022.11.28

  • modified %!like% to the more conventional !x %like% y
  • added the rm.mbr() function

1.0.2 - 2022.11.28

  • implemented S3 object for tidyproteomics data object
  • refactored all functions to accout for new data object
  • fixed minor issues with exporting data and plots
  • updated and added more vignettes

Version: beta

0.7.3 - 2022.11.15

  • modified expression() to more accurately account for the imputation ratio

0.7.2 - 2022.11.03

  • refactored plotting to utilize a generalized save function to facilitate pipelining
  • modified subset to behave like a tidyverse function while also introducing the operators like and !like to subset data based on a string matching comparison
  • updated the functions normalize(), plot_counts() and summary() that utilize subset()

0.7.1 - 2022.10.28

  • refactored import() to allow for user based configurations
  • refactored subset(), eliminating remove(), to account for value comparison and pattern matching
  • refactored reassign(), from modify(), to improve sample renaming

0.7.0 - 2022.10.15

  • added plot_quantrank()
  • fixed issue with ProteomeDiscoverer importing of TMT data

0.6.0 - 2022.09.29

  • minor bug fixes
  • refactored rollup() to collapse()
  • defined meld() and codify() to create uniformity in data import and segmentation

0.5.0 - 2022.09.23

  • created remove() and migrated subset(match_between_runs = FALSE)
  • improved protein accounting in import() and rollup() to include protein group accounting
  • added plot_counts()
  • added import(‘Skyline’, ‘peptides’), Skyline can handel DDA, PRM via MSAmanda and DIA vi DIA-Umpire
  • added import(‘DIA-NN’, ‘peptides’), DIA-NN can handel DIA

0.4.2 - 2022.09.19

  • fixed issue with “out of memory” on subset(match_between_runs = FALSE)
  • fixed an x-axis ordering bug plot_variation()
  • fixed a minor bug in importing ProteomeDiscoverer peptide data

0.4.1 - 2022.09.13

  • fixed a minor bug in importing MaxQuant data (empty data object)
  • fixed a minor bug in plot_protein()
  • fixed bug in annotations()
  • fixed bug in impute() with randomforest
  • fixed bug in expression() with limma

0.4.0 - 2022.09.08

  • added import() for MaxQuant peptides (evidence.txt)
  • added import() for MaxQuant proteins (proteinGroups.txt)
  • updated import() for ProteomeDiscoverer (better configs)

0.3.0

  • added protein rollup() function, integrated with rfasta

0.2.0

  • updated impute() accounting
  • added plot_enrichment()
  • added history of data transformations via operations()

0.1.0

  • initial cohesion of a loose collection of functions into an R package