promor 0.2.1

promor 0.2.1

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

promor 0.2.0

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

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

First release available on CRAN.