# Progression Analysis of Disease with Survival using Topological Data Analysis

## 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