An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer

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Documentation for package ‘GSgalgoR’ version 1.19.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

GSgalgoR-package	GSgalgoR: A bi-objective evolutionary meta-heuristic to identify robust transcriptomic classifiers associated with patient outcome across multiple cancer types.
calculate_distance	Functions to calculate distance matrices using cpu computing
calculate_distance_euclidean_cpu	Functions to calculate distance matrices using cpu computing
calculate_distance_pearson_cpu	Functions to calculate distance matrices using cpu computing
calculate_distance_spearman_cpu	Functions to calculate distance matrices using cpu computing
calculate_distance_uncentered_cpu	Functions to calculate distance matrices using cpu computing
callback_base_report	Print basic info per generation
callback_base_return_pop	A base callback function that returns a galgo.Obj
callback_default	A default call_back function that does nothing.
callback_no_report	Print minimal information to the user about galgo execution.
classify_multiple	Classify samples from multiple centroids
cluster_algorithm	Wrapper function to perform partition around medioids (PAM) for GalgoR
cluster_classify	Distance to centroid classifier function
cosine_similarity	Function for calculating the cosine similarity
create_centroids	Create Centroids
galgo	GSgalgoR main function
galgo.Obj	Galgo Object class
galgo.Obj-class	Galgo Object class
GSgalgoR	GSgalgoR: A bi-objective evolutionary meta-heuristic to identify robust transcriptomic classifiers associated with patient outcome across multiple cancer types.
k_centroids	Function to calculate the centroids of different groups (classes)
non_dominated_summary	Summary of the non dominated solutions
plot_pareto	Plot pareto front from an galgo.Obj
select_distance	Functions to calculate distance matrices using cpu computing
surv_fitness	Survival fitness function using the Restricted Mean Survival Time (RMST) of each group
to_dataframe	Convert galgo.Obj to data.frame
to_list	Convert galgo.Obj to list