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 implementation
N.x.x - major updates or changes that would break backward compatibility.
Version: 1.8.x
1.8.2 - 2024.08.02
- Updated the volcano plot to include auto-generated titles, classif 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