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
jeremymcrae/recessiveStats documentation built on May 17, 2017, 6:09 p.m.