jass.models.worktable

This contains all functions for accessing the "worktable" hdf5 file. All functions either create or read a worktable at a specific path location.

@author: vguillem, hmenager, hjulienne

Functions

add_signif_status_column(region_sub_tab[, ...])
binary_code(*args)	Generates the binary code of each pattern ensuring compatibility between Linux and Windows
binary_code_Big(dico_index_y, *args)	binary_code Generates the binary code of each pattern ensuring compatibility between Linux and Windows
choose_stat_function(smart_na_computation, ...)
compute_frequent_missing_pattern(sum_stat_tab)	Compute the frequency of missing pattern in the dataset
compute_frequent_missing_pattern_Big(...)	Compute the frequency of missing pattern in the dataset
compute_pleiotropy_index(W, ...)
create_genome_full_csv(project_hdf_path, ...)	Write the genome_full.csv file
create_genome_full_csv_lock_file(...)
create_worktable_file(phenotype_ids, ...[, ...])	Create a worktable file from an initial data table by specifying the selected phenotypes and the computation strategy
get_genome_full_csv_lock_path(project_hdf_path)
get_region_summary(sum_stat_tab, phenotype_ids)
get_worktable_gencov(project_hdf_path)	Read and return the summaryTable dataframe from a worktable file
get_worktable_genomedata(project_hdf_path)	Read and return the Regions dataframe from a worktable file
get_worktable_local_heatmap_data(...[, ...])	Read and return the SumStatTab dataframe from a worktable file for a given chromosome and region for the Heatmap plot
get_worktable_local_manhattan_data(...[, ...])	Read and return the SumStatTab dataframe from a worktable file for a given chromosome and region for the Manhattan plot
get_worktable_phenolist(project_hdf_path)	Read and return the PhenoList dataframe from a worktable file
get_worktable_summary(project_hdf_path)	Read and return the summaryTable dataframe from a worktable file
post_computation_filtering(worktable_chunk)	Remove SNPs that seems aberrant: SNPs with a very low p-value that are isolated
signif(x, digit)	Round a number x to represent it with <digit> digits
store_pattern(dico_z, dico_index_x, *colonne)	Reorders z-values by pattern and store their index in the original dataframe
stringize_dataframe_region_chr(dataframe)	Reformat Region and Chromosome numbers as strings in a DataFrame.