Progression Analysis of Disease with Survival using Topological Data Analysis

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Documentation for package ‘GSSTDA’ version 1.0.0

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

Help Pages

case_tag	Case-control vector
check_arg_mapper	check_arg_mapper
check_filter_values	check_filter_values
check_full_data	check_full_data
check_gene_selection	check_gene_selection
check_vectors	check_vectors
clust_all_levels	Get clusters for all data level
clust_lev	Get clusters for a particular data level
compute_node_adjacency	Computes the adjacency matrix.
cox_all_genes	Survival analysis based on gene expression levels.
denoise_rectangular_matrix	Rectangular Matrix Denoiser.
dsga	Disease-Specific Genomic Analysis
flatten_normal_tiss	Flatten normal tissues
full_data	Gene expression matrix
generate_disease_component	Generate disease component matrix.
gene_selection	Gene selection and filter function
gene_selection.default	gene_selection_classes.default
gene_selection.dsga_object	gene_selection_classes.dsga_object
gene_selection_	Private gene_selection_
gene_selection_surv	Gene selection based on variability and the relationship to survival.
get_intervals_One_D	Extract intervals from filter function output values.
gsstda	Gene Structure Survival using Topological Data Analysis (GSSTDA).
incMarPas	Incomplete Marcenko-Pastur Integral
levels_to_nodes	Extract Information about Nodes
lp_norm_k_powers_surv	Filtering function
mapper	Mapper object
map_to_color	Map to color
MedianMarcenkoPastur	Median of the Marcenko-Pastur Distribution
one_D_Mapper	one_D_Mapper
optimal_SVHT_coef_gamma_known	Optimal SVHT Coefficient with Known Noise Level
optimal_SVHT_coef_gamma_unknown	Optimal SVHT Coefficient with Unknown Noise Level
plot_dsga	plot dsga
plot_mapper	Plot mapper
results_dsga	results dsga
samples_in_levels	Samples in levels
survival_event	Survival event vector
survival_time	Survival time vector