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Update History

updates.Rmd

A condensed accounting of updates, semantic versioning.

Version: 1.7.x

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