protools2 v0.2.16

protools2 v0.2.16

1. normalize_areas... dynamic cut off column ('max_scr' default, no longer uses delta score)
2. Cut off defaults = 0

protools2 v0.2.15

protools2 v0.2.15

Fix

• impute_na handles NA (0 <- NA)
• impute_na handles single replicates (forces data.frame/matrix structure instead of default vector for single dimension)

protools2 v0.2.14

protools2 v0.2.14

Changes

• impute_na():
  • imputes within groups; when all of a group are NA use min of dataset - 1 (FIX: min defined outside loop); previously was min of file column - 1.
• normalise functions ('script_helpers.R', 'normalize functions.R'):
  • makes use of updated impute_na(), corrected legacy imputation (non-grouped) with/without log.
  • normalize_areas_return_ppindex$df.norm.log2.centered.scaled.na.imputed.new is the new main output (with log2, centre, scale).
  • normalize_areas_return_protein_groups$df.norm.log2.centered.scaled.na.imputed.new is the new main output (with log2, centre, scale).
  • Alternate NA imputation VIM::kNN with impute_na_knn() accessed via parameter k_NN, if NULL (default) impute_na(), else integer defines number of Nearest Neighbours used.
• enrichment.from.list():
  • Fixes "cannot xtfrm data frames" error.
  • Fixes filtering of 'no_mod'.
• Removed redundant installer().

protools2 v0.2.12

protools2 v0.2.12

• Bugfix:
  • Error in NAMESPACE (deleted function still exported, now removed), prevented protools2 installation.
• New impute_na() for 'normalisation functions.R':
  • normalize_areas_return_ppindex()
  • normalize_areas_return_protein_groups()
  • Replaces NA values in df.areas for the current condition with the row means calculated for each unique condition group, but if all values in the row for the current condition are NA, replace NA with the minimum value of the column - 1.

protools2 v0.2.10

protools2 v0.2.10

Corrected:

• normalize functions (correct NA imputation)
• summary_data (for new combiPeptData)
• script_helpers
• README

protools2 v0.2.9

1. Updated to now include modified functions of original protools2 package:

• Function names are identical, but appended with '_edit'
• Functions added to script_helpers.R (source: protools2/R)
• Original functions are still in place for backward-compatibility

2. Contains the recent (as of June 2023) Uniprot databases for human, mouse, rat and pig, which can be accessed like so:

• devtools2::uniprot_human
• devtools2::uniprot_mouse
• devtools2::uniprot_rat
• devtools2::uniprot_pig

protools2 v0.2.1

Proteomic analysis.