ideal-genom documentation

Welcome to the documentation of ideal-genom, a Python library for genome-related analysis.

API Reference

• GWAS with Generalized Linear Models (GLM)
  • GWASfixed
• GWAS with Generalized Linear Mixed Models (GLMM)
  • GWASrandom
• PostImputation Module
  • AnnotateVCF
  • FilterVariants
  • GetPLINK
  • IndexVCF
  • NormalizeVCF
  • ParallelTaskRunner
  • ProcessVCF
  • ReferenceNormalizeVCF
  • UnzipVCF
• Preparatory Module
  • Preparatory
• Manhattan-type Plots Module
  • compute_relative_pos()
  • find_chromosomes_center()
  • manhattan_draw()
  • manhattan_process_data()
  • manhattan_type_annotate()
  • miami_draw()
  • miami_draw_anno_lines()
  • miami_process_data()
• Other Plots Module
• Zoom-Heatmap Plot Module
  • draw_zoomed_heatmap()
  • filter_sumstats()
  • get_gene_information()
  • get_ld_matrix()
  • get_zoomed_data()
  • snp_annotations()
• Annotations Module
  • annotate_snp()
  • annotate_variants()
  • annotate_with_ensembl()
  • annotate_with_refseq()
  • get_chr_to_NC()
  • get_closest_gene()
  • get_number_to_chr()
  • gtf_to_all_genes()
  • prepare_genome()
  • prepare_gtf_path()
• API Clients
  • GeneEnsemblRestClient
  • VEPEnsemblRestClient
• Examples Module
  • get_bmi_japanese_gwas_sex_dependent()
  • get_height_japanese_gwas()
  • get_top_cond_trumpet_quantitative()
  • get_top_loci_trumpet_quantitative()
  • get_trumpet_binary_example()
  • get_trumpet_quantitative_example()
• References Module
  • AssemblyReferenceFetcher
  • Ensembl37Fetcher
  • Ensembl38Fetcher
  • FetcherLDRegions
  • RefSeqFetcher
  • ReferenceDataFetcher
• ideal_genom.Helpers
  • arg_parser()
  • delete_temp_files()
  • download_file()
  • extract_gz_file()
  • shell_do()
  • unzip_file_flat()
• Statistical Power Computation
  • calculate_power_binary()
  • calculate_power_quantitative()
  • get_beta_binary()
  • get_beta_quantitative()