Files in jeremymcrae/recessiveStats
Enrichment of recessive variants within genes
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/alleles_ddd.R
R/alleles_exac.R
R/alleles_recessive_test.R
R/calculate_autozygosity.R
R/cumulative_frequency.R
R/data.R
R/filter_by_CADD.R
R/gene_coordinates.R
R/get_polyphen.R
R/parse_vep.R
R/recessiveStats-package.R
R/set_exac_path.R
R/suspected_syndromes_test.R
R/sysdata.rda
R/tidy_variants.R
R/tweak_lofs.R
README.md
data-raw/all_gencode_genes_v19.txt.gz
data-raw/constants.R
data-raw/gencode.R
data-raw/get_gene_freqs.R
data-raw/suspected_syndrome_terms_finalise.R
data-raw/suspected_syndrome_terms_preclean.R
data-raw/syndromes_list.R
data/gencode.rda
data/syndromes_list.rda
man/SYNDROMES.Rd
man/all_enrichment.Rd
man/analyse_inherited_enrichment.Rd
man/biallelic_func_enrichment.Rd
man/biallelic_lof_enrichment.Rd
man/biallelic_syn_enrichment.Rd
man/calculate_gene_similarity.Rd
man/calculate_no_match.Rd
man/calculate_proband_similarity.Rd
man/calculate_syndrome_rates.Rd
man/check_autozygosity_in_chrom.Rd
man/check_for_last_base_in_exon.Rd
man/check_sample_autozygosity_genome_wide.Rd
man/convert_genotypes.Rd
man/cumulative_frequency.Rd
man/enrichment_multiple_populations.Rd
man/enrichment_single_population.Rd
man/filter_exac_variants_by_cadd.Rd
man/find_file_pos.Rd
man/gencode.Rd
man/get_count_combinations.Rd
man/get_cumulative_frequencies.Rd
man/get_ddd_cohort.Rd
man/get_ddd_variants_for_gene.Rd
man/get_ddd_vep_annotations.Rd
man/get_exac_variants_for_gene.Rd
man/get_exon_ends.Rd
man/get_gene_coordinates.Rd
man/get_gene_ids_for_hgnc.Rd
man/get_hemizygous.Rd
man/get_lines_from_vep_vcf.Rd
man/get_list_of_population_frequencies.Rd
man/get_most_severe_consequence.Rd
man/get_polyphen.Rd
man/get_transcript_ids_for_ensembl_gene_ids.Rd
man/lof_func_enrichment.Rd
man/open_suspected_syndromes.Rd
man/parse_vep_output.Rd
man/permute_probands.Rd
man/recessiveStats.Rd
man/reformat_chrX_genotypes.Rd
man/remove_easy_nonfunctional.Rd
man/remove_high_frequency_vars.Rd
man/remove_nonfunctional_variants.Rd
man/request_from_ensembl.Rd
man/set_exac_path.Rd
man/standardise_multiple_alt_variants.Rd
man/sum_combo_tests.Rd
man/tally_alleles.Rd
man/test_gene.Rd
scripts/analyse_recessive_gene.ddd.R
scripts/autozygosity/check_probands_autozygosity.R
scripts/autozygosity/get_autozygous_rates_per_gene.R
scripts/autozygosity/merge_vcfs.py
scripts/autozygosity/proband_autozygosity.R
scripts/check_ddd_ethnicities.R
scripts/check_syndrome_similarity.R
scripts/check_syndromes_qq_plot.R
scripts/combine_tests.R
scripts/count_recessive_familys_per_gene.R
scripts/qq_plots_for_synonymous_enrichment.R
tests/testthat.R
tests/testthat/test_cumulative_frequencies.R
tests/testthat/test_enrichment_model.R
tests/testthat/test_tidy_variants.R
tests/testthat/test_vep_parsing.R
