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promor 0.2.1

R CMD check results - 07-17-2023

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

Re-submission

In this re-submission:

  • Used bibentry() instead of citEntry() in the inst/CITATION file as suggested by the CRAN team.

Submission

R CMD check results - 07-11-2023

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

Documentation updates

  • In previous versions, the functionality of the uniq_pep parameter (see create_df help page) was incorrectly described. We corrected the description to match its functionality as follows: "Numerical. Proteins that are identified by this number or fewer number of unique peptides are filtered out (default is 2).Only applies when input_type = "MaxQuant".

Bug fixes

  • In previous versions, volcano_plot function plotted "-log10(P-value)" on the y-axis by default even when sig = "adjP" and only colored the dots by their significance based on "adjP". In this version, sig = "adjP" shows "-log10.adj. P-value" on the y-axis and colors the dots by their "adjP" significance.

promor 0.2.0

Submission

R CMD check results - 01-17-2023

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

New data types allowed

  • A new argument (data_type) added to the create_df function to accommodate other types of LFQ data (raw intensity, iBAQ).

A new input type added

  • A new argument input_type added to the create_df function to allow users to input data from a standard quantitative matrix.

Workflow changes

  • To allow for missing data imputation prior to or after data normalization step (depending on the imputation method used), the following changes were made:
    • norm_df and imp_df arguments replaced with a generic df argument in the functions, find_dep, impute_na, normalize_data, and heatmap_de
    • A note was added to the tutorials to clarify that for some imputation methods, such as the kNN method, data normalization should be performed prior to imputation.

Default machine learning algorithms

  • naive_bayes added to the default algorithm_list argument in the train_models function.

promor 0.1.1

R CMD check results - 10-27-2022

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

Re-submission

In this re-submission:

Submission

R CMD check results - 10-26-2022

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

Bug fixes

  • Fixes a minor issue with create_df when removing potential contaminants. The number of potential contaminants removed is now shown in the console.
  • Fixes an issue with find_dep that previously used a fixed value for the adj_method argument.
  • Fixes an issue with the file_path argument for saving the "TopHits.txt" file produced by the find_dep function.

Other changes

  • Citation file updated with the biorxiv preprint details.
  • Readme file updated with information on the Shiny App.
  • Help pages updated.

promor 0.1.0

Re-submission

R CMD check results - 07-19-2022

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

In this re-submission:

  • Added references to the DESCRIPTION file.
  • Limited the use of \dontrun to an example that would otherwise write to the user's working directory*
  • Added \donttest to examples that are not executable in < 5 sec and unwrapped all the remaining examples*
  • Removed unnecessary information messages that were previously written to the console*
  • Provided seed as an argument to avoid setting seed to a specific number within functions*
  • Made changes in functions to write files to tempdir() when file_path is not specified.

First submission

R CMD check results - 07-08-2022

0 errors ✔ | 0 warnings ✔ | 0 notes ✔