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
1.8.4 - 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 tonormalize()
prior tomerge()
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
1.7.3 - 2024.03.12
- fixed issue with importing FragPipe tsv files, seems to be an issue
with the
vroom
package. Modified to use thereadr
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
1.7.0 - 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
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]
1.5.2 - 2023.06.29
- bug fix in limma expression differences (name ordering only effecting data with 3+ sample groups) [thanks: github.com/tywang-tw]
1.5.0 - 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
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
Version: 1.0.x
Version: beta
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
0.6.0 - 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