CHANGES IN VERSION 1.21.2 ------------------------- BUG FIXES o add rmarkdown to DESCRIPTION CHANGES IN VERSION 1.21.1 ------------------------- UPDATE o update axis.text and theme_bw CHANGES IN VERSION 1.21.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.13 development release CHANGES IN VERSION 1.20.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.12 release CHANGES IN VERSION 1.19.3 ------------------------- UPDATE o Add link to website CHANGES IN VERSION 1.19.2 ------------------------- BUG FIXES o remove grid from Description CHANGES IN VERSION 1.19.1 ------------------------- NEW FEATURES o validate_columns update o update documentation to roxygen2 (many thanks to Ashton Trey Belew (abelew) for starting this and doing most of the work) (IS#1, PR#2, PR#3) o Some parameters were renamed to omit having a dot. E.g. rm.decoy is now called rm_decoy. If you want the previous names use SWATH2stats up to version 1.19.0 CHANGES IN VERSION 1.19.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.12 development release CHANGES IN VERSION 1.18.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.11 release CHANGES IN VERSION 1.17.5 ------------------------- update o .Rmd vignettes: remove tinytex option CHANGES IN VERSION 1.17.4 ------------------------- update o convert_protein_ids: Also count empty strings as NA and count unique non-mapped identifiers. CHANGES IN VERSION 1.17.3 ------------------------- update o plot_correlation_between_samples.R, plot_variation.R, plot_variation_vs_total.R: improve plots and do theme_bw CHANGES IN VERSION 1.17.2 ------------------------- NEW FEATURES o filter_on_min_peptides.R: add ability to deal with PeptideSequence column o filter_on_max_peptides.R: add ability to deal with PeptideSequence column CHANGES IN VERSION 1.17.1 ------------------------- UPDATE o convert_protein_ids: count unique non-mapped IDs. CHANGES IN VERSION 1.17.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.11 development release CHANGES IN VERSION 1.16.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.10 release CHANGES IN VERSION 1.15.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.10 development release CHANGES IN VERSION 1.14.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.9 release CHANGES IN VERSION 1.13.6 ------------------------- UPDATE o aLFQ is deprecated on CRAN and thus Vignette cannot depend anymore on the aLFQ package. CHANGES IN VERSION 1.13.5 ------------------------- NEW FEATURES o Update plot_variation and plot_variation_vs_total function CHANGES IN VERSION 1.13.4 ------------------------- NEW FEATURES o Update version for JPP (new version of pyprophet) CHANGES IN VERSION 1.13.3 ------------------------- UPDATE o DESCRIPTION: move PECA to enhances CHANGES IN VERSION 1.13.2 ------------------------- UPDATE o Vignette: make PECA chunk eval=FALSE to prevent error when the PECA package is not available on BioC CHANGES IN VERSION 1.13.1 ------------------------- NEW FEATURES o Add ImmunoOncology to biocViews CHANGES IN VERSION 1.13.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.9 development release CHANGES IN VERSION 1.12.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.8 release CHANGES IN VERSION 1.11.8 ------------------------- UPDATE o updating information on checking transitions in convert4aLFQ function. CHANGES IN VERSION 1.11.7 ------------------------- UPDATE o avoid sorting when adding gene symbols in add_gene_symbol CHANGES IN VERSION 1.11.6 ------------------------- BUG FIXES o fix manual page and function in convert_protein_ids to copy non-converted IDs CHANGES IN VERSION 1.11.5 ------------------------- UDPATE o move from bioclite to BiocManager CHANGES IN VERSION 1.11.4 ------------------------- BUG FIXES o fix manual page to convert_protein_ids CHANGES IN VERSION 1.11.3 ------------------------- BUG FIXES o updates to convert_protein_ids, see that convert4aLFQ outputs character vectors CHANGES IN VERSION 1.11.2 ------------------------- NEW FEATURES o add functions convert_protein_ids, load_mart, add_genesymbol CHANGES IN VERSION 1.11.1 ------------------------- BUG FIXES o remove links from manual page SWATH2stats-package CHANGES IN VERSION 1.11.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.8 development release CHANGES IN VERSION 1.10.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.7 release CHANGES IN VERSION 1.9.3 ------------------------- BUG FIXES o removed aLFQ direct link in manual CHANGES IN VERSION 1.9.2 ------------------------- NEW FEATURES o add option check_tranisitions to convert_aLFQ function o replace align_orig_filename column with filename CHANGES IN VERSION 1.9.1 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.7 development release CHANGES IN VERSION 1.8.1 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.6 release CHANGES IN VERSION 1.7.7 ------------------------- BUG FIXES o update vignette to prevent misunderstanding what data to load CHANGES IN VERSION 1.7.6 ------------------------- BUG FIXES o manual convert4PECA CHANGES IN VERSION 1.7.5 ------------------------- BUG FIXES o library not recognized in vignette CHANGES IN VERSION 1.7.4 ------------------------- NEW FEATURES o add function convert4PECA CHANGES IN VERSION 1.7.3 ------------------------- NEW FEATURES o add option to keep all columns to disaggregate function CHANGES IN VERSION 1.7.2 ------------------------- NEW FEATURES o add option to no not remove decoys to filter_proteotypic_peptides(), filter_on_max_peptides(), and filter_on_min_peptides() CHANGES IN VERSION 1.7.1 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.6 development release CHANGES IN VERSION 1.6.1 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.5 release CHANGES IN VERSION 1.5.8 ------------------------- NEW FEATURES o filter_on_max_peptides: add removeDecoyProteins and unifyProteinGroupLabels to function o filter_on_min_peptides: add removeDecoyProteins and unifyProteinGroupLabels to function BUG FIXES o filter_on_max_peptides: unique selected peptides to prevent duplication of rows CHANGES IN VERSION 1.5.7 ------------------------- NEW FEATURES o featurealigner2msstats_withRT.py: reads now csv and tab delimited file and checks for right data structure CHANGES IN VERSION 1.5.6 ------------------------- NEW FEATURES o plot.fdr_cube: add option to select mscore levels to plot FDR estimation. o assess_fdr_byrun: add option to select mscore levels to plot FDR estimation. CHANGES IN VERSION 1.5.5 ------------------------- NEW FEATURES o sample_annotation: added "fixed" option to grep function to increase speed. BUG FIXES o convert4mapDIA: diagnostic output in case there were several values was not displaying correct rows. CHANGES IN VERSION 1.5.4 ------------------------- BUG FIXES o removeDecoyProteins and unifyProteinGroupLabels: fixed bug that affected protein groups of 10-19 proteins. CHANGES IN VERSION 1.5.3 ------------------------- NEW FEATURES o plot_variation: make function to work also if comparison contains more than 3 elements o plot_variation_vs_total: make function to work also if comparison contains more than 3 elements o sample_annotation: introduce fail-safe if input data is in the data.table format. CHANGES IN VERSION 1.5.2 ------------------------- NEW FEATURES o unifyProteinGroupLabels: unifies different ProteinGroupLabels o removeDecoyProteins, rmDecoyProt: Removes decoy protein labels from protein Group label CHANGES IN VERSION 1.5.1 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.5 development release CHANGES IN VERSION 1.4.1 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.4 release CHANGES IN VERSION 1.3.10 ------------------------- BUG FIXES o sample_annotation: add stop if column for files is not present, instead of printing a warning o convert4aLFQ: improve warning message o tests: add tests CHANGES IN VERSION 1.3.9 ------------------------- NEW FEATURES o sample_annotation: improved architecture of function o tests: add tests o MSstats_data: add data in MSstats format to use for testing o assess_decoy_rate: add stop instead of warnings if no decoy column is present o mscore4pepfdr, mscore4assayfdr: add default value in function description CHANGES IN VERSION 1.3.8 ------------------------- BUG FIXES o DESCRIPTION: move MSstats from suggests to enhances CHANGES IN VERSION 1.3.7 ------------------------- BUG FIXES o test_filtering: tests for count_analytes CHANGES IN VERSION 1.3.6 ------------------------- NEW FEATURES o filter_all_peptides: Improvement in display of protein Names using collapse DOCUMENTATION o Vignette: make MSstats and aLFQ eval=FALSE to prevent error when these are not build properly CHANGES IN VERSION 1.3.5 ------------------------- NEW FEATURES o filter_mscore_fdr: add fail-safe in case target protein FDR cannot be reached. o plot_variation, plot_variation_vs_total, plot_correlation_between_samples, count_analytes: add tests CHANGES IN VERSION 1.3.4 ------------------------- NEW FEATURES o convert4mapDIA: improve error message in the case that multiple values exist per condition o plot_correlation_between_samples: add option to not write any labels BUG FIXES o plot_variation: improved function to also deal with data that did not have the same size in the different conditions DOCUMENTATION o DESCRIPTION: update packages to import o convert4MSstats: updated warning message CHANGES IN VERSION 1.3.3 ------------------------- BUG FIXES o Add fail-safe functionality to sample_annotation function for non-unique file names. CHANGES IN VERSION 1.3.0 ------------------------- NEW FEATURES o Development version of SWATH2stats in BioC 3.4 CHANGES IN VERSION 1.2.3 ------------------------- BUG FIXES o Add fail-safe functionality to sample_annotation function for non-unique file names. CHANGES IN VERSION 1.2.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.3 release CHANGES IN Version 1.1.17 ------------------------- DOCUMENTATION o updated NEWS file CHANGES IN Version 1.1.16 ------------------------- BUG FIXES o Error fix in test_convert.R CHANGES IN Version 1.1.15 ------------------------- DOCUMENTATION o Add Citation of PLoS ONE publication of SWATH2stats CHANGES IN VERSION 1.1.14 ------------------------- DOCUMENTATION o import_data: minor changes in documentation o defining several functions at the beginning of function script CHANGES IN VERSION 1.1.13 ------------------------- DOCUMENTATION o assess_fdr_byrun, assess_fdr_overall, filter_mscore_fdr: add sentence to manual page about FFT o vignettes: Add/change title BUG FIXES o DESCRIPTION: add knitr to Suggests and VignetteBuilder, add R>=2.10.0 to Depends CHANGES IN VERSION 1.1.12 ------------------------- NEW FEATURES o sample_annotation: remove option column.runid. o assess_fdr_byrun and assess_fdr_overall: add option to set range of plotting with n.range DOCUMENTATION o SWATH2stats_example_script, Spyogenes data: added Example script and S.pyogenes data CHANGES IN VERSION 1.1.11 ------------------------- NEW FEATURES o plot_correlation_between_samples: import cor function from stats package and reorder y axis. CHANGES IN VERSION 1.1.10 ------------------------- BUG FIXES o test for FDR filtering: bug fix due to fix in mscore4assayfdr CHANGES IN VERSION 1.1.9 ------------------------- DOCUMENTATION o Update vignette DEPRECATED AND DEFUNCT o remove function: filter_all_peptides BUG FIXES o mscore4assayfdr: bug fix CHANGES IN VERSION 1.1.8 ------------------------- BUG FIXES o add functions that were not updated CHANGES IN VERSION 1.1.7 ------------------------- NEW FEATURES o added functions: count_analytes, plot_correlation_between_samples, plot_variation, plot_variation_vs_total, transform_MSstats_OpenSWATH. o filter_mscore_requant renamed to filter_mscore_freqobs BUG FIXES o sample_annotation: Bug fix - it reported upon error different conditions instead of filenames. o assess_fdr_overall: Correction of transition level column name from "id" to "transition_group_id" o assess_fdr_byrun: Correction of transition level column name from "id" to "transition_group_id" o plot.fdr_cube: added na.rm=TRUE to plotting functions CHANGES IN VERSION 1.1.6 ------------------------- BUG FIXES o Correction of typographical error in Vignette for Wolski et al. CHANGES IN VERSION 1.1.5 ------------------------- BUG FIXES o Bug fixes for assess_fdr_byrun that was also introduced into version v1.0.2 at the same time. It fixes problems with labelling the runs correctly in some cases. CHANGES IN VERSION 1.1.4 ------------------------- BUG FIXES o Bug fixes in test_convert. CHANGES IN VERSION 1.1.1 ------------------------- NEW FEATURES o Improved the function disaggregate() that also data with different number of transitions per precursor than 6 can be used o Added tests for disaggregate.R and convert4pythonscript.R CHANGES IN VERSION 1.1.0 ------------------------- NEW FEATURES o Development version of SWATH2stats in BioC 3.3 CHANGES IN VERSION 1.0.0 ------------------------- NEW FEATURES o SWATH2stats in BioC 3.2 release CHANGES IN VERSION 0.99.5 ------------------------- NEW FEATURES o SWATH2stats package accepted to Bioconductor