# Two-Tier Mapper: a clustering tool based on topological data analysis

## Documentation for package ‘TTMap’ version 1.31.0

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

## Help Pages

TTMap-package | Two-Tier Mapper: a clustering tool based on topological data analysis
calcul_e | Calculation of the value of epsilon
calcul_e_single | Calculation of the value of epsilon
control_adjustment | Calculates a corrected control group, discovers outliers in it.
generate_correlation | Generates different distance matrices
generate_euclidean | Generates different distance matrices
generate_mismatch_distance | Generates different distance matrices
generate_p_val_correlation | Generates different distance matrices
generate_single_cell_complete_mismatch | Generates different distance matrices
generate_single_cell_mismatch_with_parameter | Generates different distance matrices
hyperrectangle_deviation_assessment | Calculation of deviation components
make_matrices | Prepares the matrices for 'control_adjustment'
make_matrices-method | Prepares the matrices for 'control_adjustment'
make_matrices-methods | Prepares the matrices for 'control_adjustment'
mat2pcl | Reading, writing and annotation files
read_pcl | Reading, writing and annotation files
TTMap | Two-Tier Mapper: a clustering tool based on topological data analysis
ttmap | Visualisation of the clustering
ttmap_sgn_genes | Gives a list of associated genes per cluster
ttmap_sgn_genes_inter | Gives a list of associated genes per cluster
ttmap_sgn_genes_inter2 | Gives a list of associated genes per cluster
write_pcl | Reading, writing and annotation files