Man pages for jeremymcrae/recessiveStats
Enrichment of recessive variants within genes
| all_enrichment | test enrichment of inherited biallelic LoF, compound... |
| analyse_inherited_enrichment | test for enrichment of inherited variants |
| biallelic_func_enrichment | test enrichment of inherited biallelic functional variants |
| biallelic_lof_enrichment | test for enrichment of biallelic LoF inherited variants |
| biallelic_syn_enrichment | test enrichment of inherited biallelic synonymous variants |
| calculate_gene_similarity | calculate the similarity of suspected syndrome terms within a... |
| calculate_no_match | calculate the proportion of samples with no matches |
| calculate_proband_similarity | calculate the similarity of suspected syndromes between two... |
| calculate_syndrome_rates | calculate the rate at which each syndrome term is used within... |
| check_autozygosity_in_chrom | identify chromosomal regions where a proband has... |
| check_for_last_base_in_exon | modifies the consequence where the variant is at the last... |
| check_sample_autozygosity_genome_wide | identify the genome regions where a proband has... |
| convert_genotypes | reformats the genotypes dataset |
| cumulative_frequency | calculate cumulative allele frequency from a vector of allele... |
| enrichment_multiple_populations | test for enrichment of inherited variants in multiple... |
| enrichment_single_population | test for enrichment of inherited variants |
| filter_exac_variants_by_cadd | filter ExAC variants by CADD score |
| find_file_pos | find where the required data lies within the file |
| gencode | table of genecode gene coordinates |
| get_count_combinations | Get all the combinations of spreading the probands across... |
| get_cumulative_frequencies | obtain cumulative allele frequency of rare lof and functional... |
| get_ddd_cohort | get the details of the DDD cohort |
| get_ddd_variants_for_gene | loads the variants for a given gene from source VCFs |
| get_ddd_vep_annotations | gets the DDD VEP annotations for variants |
| get_exac_variants_for_gene | get and parse ExAC variants within a gene |
| get_exon_ends | gets all exon end positions for an HGNC symbol |
| get_gene_coordinates | get the genomic coordinates for a gene from an internal... |
| get_gene_ids_for_hgnc | gets the gene IDs for HGNC symbols |
| get_hemizygous | reformat to hemizygous chrX genotypes in a single column |
| get_lines_from_vep_vcf | loads DDD VEP annotations lines for variants |
| get_list_of_population_frequencies | create a list of allele frequency dataframes for each... |
| get_most_severe_consequence | get the most severe VEP consequence form a list of... |
| get_polyphen | get a polyphen prediction for a variant |
| get_transcript_ids_for_ensembl_gene_ids | gets the transcript IDs for ensembl gene IDs |
| lof_func_enrichment | test enrichment of inherited biallelic LoF and compound... |
| open_suspected_syndromes | open suspected syndromes |
| parse_vep_output | parses VEP output |
| permute_probands | permutes the probands between genes |
| recessiveStats | recessiveStats: examines enrichment of recesive variants... |
| reformat_chrX_genotypes | reformat chrX genotypes for males to hemizygous |
| remove_easy_nonfunctional | quickly strips out the variants which are obviously... |
| remove_high_frequency_vars | remove high frequency variants from the dataset |
| remove_nonfunctional_variants | exclude nonfunctional variants, or nonfunctional alleles of... |
| request_from_ensembl | make a URL request to the Ensembl service |
| set_exac_path | sets the path to the ExAC dataset files |
| standardise_multiple_alt_variants | tidy up a variant dataset, so that multiple alt variants are... |
| sum_combo_tests | get a p-value that sums across different population... |
| SYNDROMES | table of syndromes, with regexes to match in the probands... |
| tally_alleles | count alleles for a variant |
| test_gene | get the chance of a group of probands sharing their syndrome... |
