Package index • semseeker

All functions
`PROBES`	PROBES_CHR_CHR
`PROBES_CHR_CHR`	PROBES_CHR_CHR
`analyze_population()`	Calculate stochastic epi mutations from a methylation dataset as outcome report of pivot
`analyze_single_sample()`	analyze_single_sample
`annotate_bed()`	create an annotated file for each marker, figure, area and subarea, each file has all the sample_groups used to calculate epimutation
`apply_stat_model()`	Title
`association_analysis()`	Association analysis of SEMseeker's results
`bayes_analysis()`	P_to_be_Case_cond_to_be_Epimutated and sensibility analysis of SEMseeker's mutations and lesions
`build_data_set_from_geo()`	build_data_set_from_geo
`compute_mean_delta_permutation_cpu()`	Title
`compute_quantile_delta_permutation()`	Title
`compute_quantreg_permutation()`	Title
`compute_spearman_permutation()`	Title
`create_heatmap()`	create_heatmap load the multiple bed resulting from analysis organized into files and folders per marker and produce a pivot
`data_preparation()`	Title
`delta_single_sample()`	delta_single_sample
`deltar_single_sample()`	delta_single_sample
`dir_check_and_create()`	dir_check_and_create
`dump_sample_as_bed_file()`	given data and colnames dump as bed file
`exact_pvalue()`	Quantile regression result value, confidence interval and p.value
`glm_model()`	Title
`init_env()`	init ssEnvonment
`manhattan_plot_marker_per_probe()`	Title manhattan_plot_marker_per_probe
`manhattan_plot_marker_per_sample()`	Title manhattan_plot_marker_per_sample
`manhattan_plot_per_area()`	Title
`marker_quantization_metric_q_search()`	calculate scores for a study across all the used quantile/bin number with result saved into a base folder
`markers_performance_association_q_search()`	calculate scores for th e same dataset at changing of quantile/bins
`mean_permutation()`	Title
`mutations_get()`	mutations_get
`pivot_to_long_format()`	Get the pivot in long format instead of wide format
`pp_tot`	PROBES_CHR_CHR
`quantile_permutation_model()`	quantile_permutation_model calculate differences between the same quantile of two distribution
`quantreg_model()`	Title
`quantreg_permutation_model()`	Title
`read_multiple_bed()`	read multiple bed with annotated data as per input parameter
`search_phenotype()`	Search OMIM
`semseeker()`	Calculate Stochastic Epigenetic Mutations from a Methylation Dataset
`signal_range_values()`	calculate the range of signal values to define the outlier
`signal_single_sample()`	signal_single_sample
`sort_by_chr_and_start()`	sort the dataframe using CHR and START sorting column first for CHR and after for START
`spearman_permutation()`	Title
`ss_analysis()`	sensitivity and sensibility analysis of SEMseeker's mutations and lesions
`test_match_order()`	Title
`test_model()`	Title

Reference

All functions