v.1.2.5

• fixes: when factor levels are substrings, e.g., "m", "mm", "mmm" there was a bug in creating the linear functions for contrast computation. This problem is fixed.
• We moved more examples to use simulated data:
  • code to create linear and mixed models with one or two factors.
  • additional tests for linear function creation.
  • The prebuild package size (with vignettes and documentation) was reduced to 22.72 MB.
• Updated 2-factor vignette to include examples with modeling with subgroups, e.g., 'A_X', 'A_Y', 'B_X', 'B_Y' instead of using factors A, B, and X, Y and the interaction term.

v.1.2.4

• Fixes bug reported in issue #71
• Implements changes for issue #70 (improved modelling of missing contrasts, by using weighted LOD).

to install this release run:

install.packages("https://github.com/fgcz/prolfqua/releases/download/v.1.2.4/prolfqua_1.2.4.tar.gz", repos = NULL)

v.1.2.0

This release removes the SaintExpress binaries and functionality related to SaintExpress and moves it to the proquasaint R package.
https://github.com/prolfqua/proquasaint

to install this release:

install.packages("https://github.com/fgcz/prolfqua/releases/download/v.1.2.0/prolfqua_1.2.0.tar.gz", repos = NULL)

Full Changelog: v.1.1.5...v.1.2.0

v.1.1.5 Improving modelling missing data

• Reworked modeling of missing data using glm's.
• Added function for simulating test data.
• minor changes, e.g., additional parameters to volcano plot function.

To install

install.packages("https://github.com/fgcz/prolfqua/releases/download/v.1.1.5/prolfqua_1.1.5.tar.gz", repos = NULL)

v1.1.3 minor

Minor changes, only, development is currently concentrating on the prolfquapp package.

v1.1.2 Usability improvements

Changes:

• improved error messages in the setup_analysis function
• other improvements to the setup_analysis function, e.g., casting numeric factors to character
• refactoring to keep up with changes to dplyr e.g., spread -> pivot_wider
• get tidy_FragPipe_combined_protein working with the 19.1 version of FragPipe
• new function percentage_abundance in LFQDataSummarizer class
• new functions to create upset R plots.

Installation, including all dependencies:

#R (>=4.1)
install.packages('remotes')
remotes::install_github("https://github.com/fgcz/prolfqua/releases/tag/v1.1.2", dependencies=TRUE, build_vignettes = TRUE)

ACS_JPR_V3 V1.1.0

The associated manuscript is available on the bioRxiv preprint server through BIORXIV/2022/494524.

Major:

• Changed the name of the class ContrastsSimpleImpute to ContrastsMissing

Installation, including all dependencies

#R (>=4.1)
install.packages('remotes')
remotes::install_github("https://github.com/fgcz/prolfqua/releases/tag/v1.1.0", dependencies=TRUE, build_vignettes = TRUE)

to make use of pre-build vignette files via browseVignettes('prolfqua') execute the following command again:

install.packages('https://github.com/fgcz/prolfqua/releases/download/v1.1.0/prolfqua_1.1.0.tar.gz', repos = NULL)

ACS_JPR_V2 V1.0.0

This release will break compatibility with previous versions.

This release accompanies the submission of the revised article to ACS JPR.
The associated manuscript is available on the bioRxiv preprint server through BIORXIV/2022/494524.

Major:

• Class names are consistently CamelCase, while functions are snake_case.
• Code coverage for examples

Install:
including all dependencies

#R (>=4.1)
remotes::install_github("https://github.com/fgcz/prolfqua/releases/tag/v1.0.0", dependencies=TRUE, build_vignettes = TRUE)

to make use of pre-build vignette files via browseVignettes('prolfqua') execute the following command again:

install.packages('https://github.com/fgcz/prolfqua/releases/download/v1.0.0/prolfqua_1.0.0.tar.gz', repos = NULL)

ACS_JPR

This release accompanies the submission to ACS JPR. The associated manuscript is available on the bioRxiv preprint server through BIORXIV/2022/494524.

Minor:

• Fix QC Sample size report when the sample size in QC run is set to 1

Install:

including all dependencies

#R (>=4.1)
remotes::install_github("https://github.com/fgcz/prolfqua/releases/tag/v0.4.3", dependencies=TRUE, build_vignettes = TRUE)

to make use of pre-build vignette files via browseVignettes('prolfqua') execute the following command again:

install.packages('https://github.com/fgcz/prolfqua/releases/download/v0.4.3/prolfqua_0.4.3.tar.gz', repos = NULL)

Rename MSFragger to FragPipe

Changes:

• Renames functions for reading FragPipe output to tidy_FragPipe_
  for details:
  https://fgcz.github.io/prolfqua/reference/FragPipe.html
  See discussion #31

• Vignette "Quality Control & Sample Size Estimation" now uses R6 API

• Added "Model with Interaction" vignette based on IonStar dataset
  https://fgcz.github.io/prolfqua/articles/ModelWithInteractions.html

Install

install.packages("https://github.com/fgcz/prolfqua/releases/download/v0.4.2/prolfqua_0.4.2.tar.gz",
	repos = NULL)