Man pages for jeremymcrae/publishedDeNovos
Published De Novos Dataset from Developmental Disorder Sequencing Studies
| autism_de_novos | get de novo data from autism exome studies |
| cohorts | Cohort information. |
| deligt_de_novos | get de novo data for De Ligt et al. intellectual disability... |
| de_rubeis_de_novos | get de novo data from the 2014 De Rubeis et al. autism exome... |
| epi4k_de_novos | get de novo data for the Epi4K epilepsy exome study |
| find_matching_sites | this identifies variants which match the current row |
| find_most_severe_transcript | find the most severe transcript from Ensembl data |
| fix_coordinates | extract genomic coordinates for variants from a dataframe |
| fix_coordinates_with_allele | extract genomic coordinates for variants from a dataframe |
| fix_coordinates_with_hgvs_genomic | extract genomic coordinates for variants encoded as HGVS... |
| fix_del_alleles | fix deletion allele codes |
| fix_dup_alleles | fix duplication allele codes |
| fix_het_alleles | correct alt alleles which have been encoded as an IUPAC... |
| fix_ins_alleles | fix insertion allele codes |
| fix_sub_alleles | fix substitution allele codes |
| fix_zaiidi_coordinates | extract genomic coordinates for variants from a dataframe |
| fromer_de_novos | get de novo data from Fromer et al. schizophrenia exome study |
| get_deligt_denovo_table | load the supplementary table for the de ligt de novo variants |
| get_deligt_sex | load the supplementary table for the de ligt sex information |
| get_deligt_text | load the supplementary data for the de ligt de novos |
| get_gene_id_for_variant | find the hgnc symbol overlapping a variant position |
| get_protein_length | find the coding length for a ensembl transcript |
| get_sequence_in_region | find genomic sequence within a region |
| get_vep_consequence | find the VEP consequence for a variant |
| gilissen_de_novos | get de novo data for Gilissen et al. intellectual disability... |
| iossifov_nature_de_novos | get de novo data from the 2014 Iossifov et al. autism exome... |
| iossifov_neuron_de_novos | get de novo data from the 2012 Iossifov et al autism exome... |
| lelieveld_de_novos | get de novo data for Lelieveld et al. intellectual disability... |
| map_coordinates | map coordiantes from one assembly to another |
| oroak_de_novos | get de novo data from the O'Roak et al autism exome study |
| rauch_de_novos | get de novo data for Rauch et al. intellectual disability... |
| remove_duplicates | remove duplicate variants from the same individual |
| request_from_ensembl | make a URL request to the Ensembl service |
| sanders_de_novos | get de novo data from the Sanders et al autism exome study |
| variants | De novos from published studies. |
| zaidi_de_novos | get de novo data from Zaidi et al. congenital heart disease... |
