Features_MinimumFeatures: The minimum set of the most important features.

In masato-ogishi/Repitope: Epitope immunogenicity prediction through in silico TCR-peptide contact potential profiling

The minimum set of the most important features.

Description

Features_MinimumFeatures automates the feature selection workflows, i.e. preprocessing, filtering by correlation, filtering by importance, extract shared features from ascending vs descending models.

Usage

Features_MinimumFeatures(
  featureDFList,
  metadataDF,
  seedSet = 1:5,
  corThreshold = 0.75,
  featureNSet = 100,
  criteria = "intersect",
  returnImpDFList = T
)

Arguments

featureDFList	A list of feature dataframes generated by Features, or imported by readFeatureDFList.
metadataDF	A dataframe containing metadata, consisting of "Peptide", "Immunogenicity", and "Cluster" columns.
seedSet	A set of random seeds.
corThreshold	The threshold of correlation to eliminate features.
featureNSet	The number of the features that should be retained. Can also be a vector of numbers. In that case, a list of minimum sets of features would be returned.
criteria	The criteria of feature extraction. Can either be "intersect" or "union".
returnImpDFList	Logical. Whether the lists of feature importance dataframes should be returned as well.

masato-ogishi/Repitope documentation built on Feb. 14, 2023, 5:47 a.m.