NEWS

---

SWATH2stats 1.21.2

BUG FIXES

• add rmarkdown to DESCRIPTION

SWATH2stats 1.21.1

UPDATE

• update axis.text and theme_bw

SWATH2stats 1.21.0

NEW FEATURES

• SWATH2stats in BioC 3.13 development release

SWATH2stats 1.20.0

NEW FEATURES

• SWATH2stats in BioC 3.12 release

SWATH2stats 1.19.3

UPDATE

• Add link to website

SWATH2stats 1.19.2

BUG FIXES

• remove grid from Description

SWATH2stats 1.19.1

NEW FEATURES

• validate_columns

update

• 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)
• 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

SWATH2stats 1.19.0

NEW FEATURES

• SWATH2stats in BioC 3.12 development release

SWATH2stats 1.18.0

NEW FEATURES

• SWATH2stats in BioC 3.11 release

SWATH2stats 1.17.5

update

• .Rmd vignettes: remove tinytex option

SWATH2stats 1.17.4

update

• convert_protein_ids: Also count empty strings as NA and count unique non-mapped identifiers.

SWATH2stats 1.17.3

update

• plot_correlation_between_samples.R, plot_variation.R, plot_variation_vs_total.R: improve plots and do theme_bw

SWATH2stats 1.17.2

NEW FEATURES

• filter_on_min_peptides.R: add ability to deal with PeptideSequence column
• filter_on_max_peptides.R: add ability to deal with PeptideSequence column

SWATH2stats 1.17.1

UPDATE

• convert_protein_ids: count unique non-mapped IDs.

SWATH2stats 1.17.0

NEW FEATURES

• SWATH2stats in BioC 3.11 development release

SWATH2stats 1.16.0

NEW FEATURES

• SWATH2stats in BioC 3.10 release

SWATH2stats 1.15.0

NEW FEATURES

• SWATH2stats in BioC 3.10 development release

SWATH2stats 1.14.0

NEW FEATURES

• SWATH2stats in BioC 3.9 release

SWATH2stats 1.13.6

UPDATE

• aLFQ is deprecated on CRAN and thus Vignette cannot depend anymore on the aLFQ package.

SWATH2stats 1.13.5

NEW FEATURES

• Update plot_variation and plot_variation_vs_total function

SWATH2stats 1.13.4

NEW FEATURES

• Update version for JPP (new version of pyprophet)

SWATH2stats 1.13.3

UPDATE

• DESCRIPTION: move PECA to enhances

SWATH2stats 1.13.2

UPDATE

• Vignette: make PECA chunk eval=FALSE to prevent error when the PECA package is not available on BioC

SWATH2stats 1.13.1

NEW FEATURES

• Add ImmunoOncology to biocViews

SWATH2stats 1.13.0

NEW FEATURES

• SWATH2stats in BioC 3.9 development release

SWATH2stats 1.12.0

NEW FEATURES

• SWATH2stats in BioC 3.8 release

SWATH2stats 1.11.8

UPDATE

• updating information on checking transitions in convert4aLFQ function.

SWATH2stats 1.11.7

UPDATE

• avoid sorting when adding gene symbols in add_gene_symbol

SWATH2stats 1.11.6

BUG FIXES

• fix manual page and function in convert_protein_ids to copy non-converted IDs

SWATH2stats 1.11.5

UDPATE

• move from bioclite to BiocManager

SWATH2stats 1.11.4

BUG FIXES

• fix manual page to convert_protein_ids

SWATH2stats 1.11.3

BUG FIXES

• updates to convert_protein_ids, see that convert4aLFQ outputs character vectors

SWATH2stats 1.11.2

NEW FEATURES

• add functions convert_protein_ids, load_mart, add_genesymbol

SWATH2stats 1.11.1

BUG FIXES

• remove links from manual page SWATH2stats-package

SWATH2stats 1.11.0

NEW FEATURES

• SWATH2stats in BioC 3.8 development release

SWATH2stats 1.10.0

NEW FEATURES

• SWATH2stats in BioC 3.7 release

SWATH2stats 1.9.3

BUG FIXES

• removed aLFQ direct link in manual

SWATH2stats 1.9.2

NEW FEATURES

• add option check_tranisitions to convert_aLFQ function
• replace align_orig_filename column with filename

SWATH2stats 1.9.1

NEW FEATURES

• SWATH2stats in BioC 3.7 development release

SWATH2stats 1.8.1

NEW FEATURES

• SWATH2stats in BioC 3.6 release

SWATH2stats 1.7.7

BUG FIXES

• update vignette to prevent misunderstanding what data to load

SWATH2stats 1.7.6

BUG FIXES

• manual convert4PECA

SWATH2stats 1.7.5

BUG FIXES

• library not recognized in vignette

SWATH2stats 1.7.4

NEW FEATURES

• add function convert4PECA

SWATH2stats 1.7.3

NEW FEATURES

• add option to keep all columns to disaggregate function

SWATH2stats 1.7.2

NEW FEATURES

• add option to no not remove decoys to filter_proteotypic_peptides(), filter_on_max_peptides(), and filter_on_min_peptides()

SWATH2stats 1.7.1

NEW FEATURES

• SWATH2stats in BioC 3.6 development release

SWATH2stats 1.6.1

NEW FEATURES

• SWATH2stats in BioC 3.5 release

SWATH2stats 1.5.8

NEW FEATURES

• filter_on_max_peptides: add removeDecoyProteins and unifyProteinGroupLabels to function
• filter_on_min_peptides: add removeDecoyProteins and unifyProteinGroupLabels to function

BUG FIXES

• filter_on_max_peptides: unique selected peptides to prevent duplication of rows

SWATH2stats 1.5.7

NEW FEATURES

• featurealigner2msstats_withRT.py: reads now csv and tab delimited file and checks for right data structure

SWATH2stats 1.5.6

NEW FEATURES

• plot.fdr_cube: add option to select mscore levels to plot FDR estimation.
• assess_fdr_byrun: add option to select mscore levels to plot FDR estimation.

SWATH2stats 1.5.5

NEW FEATURES

• sample_annotation: added "fixed" option to grep function to increase speed.

BUG FIXES

• convert4mapDIA: diagnostic output in case there were several values was not displaying correct rows.

SWATH2stats 1.5.4

BUG FIXES

• removeDecoyProteins and unifyProteinGroupLabels: fixed bug that affected protein groups of 10-19 proteins.

SWATH2stats 1.5.3

NEW FEATURES

• plot_variation: make function to work also if comparison contains more than 3 elements
• plot_variation_vs_total: make function to work also if comparison contains more than 3 elements
• sample_annotation: introduce fail-safe if input data is in the data.table format.

SWATH2stats 1.5.2

NEW FEATURES

• unifyProteinGroupLabels: unifies different ProteinGroupLabels
• removeDecoyProteins, rmDecoyProt: Removes decoy protein labels from protein Group label

SWATH2stats 1.5.1

NEW FEATURES

• SWATH2stats in BioC 3.5 development release

SWATH2stats 1.4.1

NEW FEATURES

• SWATH2stats in BioC 3.4 release

SWATH2stats 1.3.10

BUG FIXES

• sample_annotation: add stop if column for files is not present, instead of printing a warning
• convert4aLFQ: improve warning message
• tests: add tests

SWATH2stats 1.3.9

NEW FEATURES

• sample_annotation: improved architecture of function
• tests: add tests
• MSstats_data: add data in MSstats format to use for testing
• assess_decoy_rate: add stop instead of warnings if no decoy column is present
• mscore4pepfdr, mscore4assayfdr: add default value in function description

SWATH2stats 1.3.8

BUG FIXES

• DESCRIPTION: move MSstats from suggests to enhances

SWATH2stats 1.3.7

BUG FIXES

• test_filtering: tests for count_analytes

SWATH2stats 1.3.6

NEW FEATURES

• filter_all_peptides: Improvement in display of protein Names using collapse

DOCUMENTATION

• Vignette: make MSstats and aLFQ eval=FALSE to prevent error when these are not build properly

SWATH2stats 1.3.5

NEW FEATURES

• filter_mscore_fdr: add fail-safe in case target protein FDR cannot be reached.
• plot_variation, plot_variation_vs_total, plot_correlation_between_samples, count_analytes: add tests

SWATH2stats 1.3.4

NEW FEATURES

• convert4mapDIA: improve error message in the case that multiple values exist per condition
• plot_correlation_between_samples: add option to not write any labels

BUG FIXES

• plot_variation: improved function to also deal with data that did not have the same size in the different conditions

DOCUMENTATION

• DESCRIPTION: update packages to import
• convert4MSstats: updated warning message

SWATH2stats 1.3.3

BUG FIXES

• Add fail-safe functionality to sample_annotation function for non-unique file names.

SWATH2stats 1.3.0

NEW FEATURES

• Development version of SWATH2stats in BioC 3.4

SWATH2stats 1.2.3

BUG FIXES

• Add fail-safe functionality to sample_annotation function for non-unique file names.

SWATH2stats 1.2.0

NEW FEATURES

• SWATH2stats in BioC 3.3 release

SWATH2stats 1.1.17

DOCUMENTATION

• updated NEWS file

SWATH2stats 1.1.16

BUG FIXES

• Error fix in test_convert.R

SWATH2stats 1.1.15

DOCUMENTATION

• Add Citation of PLoS ONE publication of SWATH2stats

SWATH2stats 1.1.14

DOCUMENTATION

• import_data: minor changes in documentation
• defining several functions at the beginning of function script

SWATH2stats 1.1.13

DOCUMENTATION

• assess_fdr_byrun, assess_fdr_overall, filter_mscore_fdr: add sentence to manual page about FFT
• vignettes: Add/change title

BUG FIXES

• DESCRIPTION: add knitr to Suggests and VignetteBuilder, add R>=2.10.0 to Depends

SWATH2stats 1.1.12

NEW FEATURES

• sample_annotation: remove option column.runid.
• assess_fdr_byrun and assess_fdr_overall: add option to set range of plotting with n.range

DOCUMENTATION

• SWATH2stats_example_script, Spyogenes data: added Example script and S.pyogenes data

SWATH2stats 1.1.11

NEW FEATURES

• plot_correlation_between_samples: import cor function from stats package and reorder y axis.

SWATH2stats 1.1.10

BUG FIXES

• test for FDR filtering: bug fix due to fix in mscore4assayfdr

SWATH2stats 1.1.9

DOCUMENTATION

• Update vignette

DEPRECATED AND DEFUNCT

• remove function: filter_all_peptides

BUG FIXES

• mscore4assayfdr: bug fix

SWATH2stats 1.1.8

BUG FIXES

• add functions that were not updated

SWATH2stats 1.1.7

NEW FEATURES

• added functions: count_analytes, plot_correlation_between_samples, plot_variation, plot_variation_vs_total, transform_MSstats_OpenSWATH.
• filter_mscore_requant renamed to filter_mscore_freqobs

BUG FIXES

• sample_annotation: Bug fix - it reported upon error different conditions instead of filenames.
• assess_fdr_overall: Correction of transition level column name from "id" to "transition_group_id"
• assess_fdr_byrun: Correction of transition level column name from "id" to "transition_group_id"
• plot.fdr_cube: added na.rm=TRUE to plotting functions

SWATH2stats 1.1.6

BUG FIXES

• Correction of typographical error in Vignette for Wolski et al.

SWATH2stats 1.1.5

BUG FIXES

• 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.

SWATH2stats 1.1.4

BUG FIXES

• Bug fixes in test_convert.

SWATH2stats 1.1.1

NEW FEATURES

• Improved the function disaggregate() that also data with different number of transitions per precursor than 6 can be used
• Added tests for disaggregate.R and convert4pythonscript.R

SWATH2stats 1.1.0

NEW FEATURES

• Development version of SWATH2stats in BioC 3.3

SWATH2stats 1.0.0

NEW FEATURES

• SWATH2stats in BioC 3.2 release

SWATH2stats 0.99.5

NEW FEATURES

• SWATH2stats package accepted to Bioconductor