data-raw/retrieve_genome_info.R

In jlaffy/infercna: Infer Copy Number Alterations And Clonality In (Single-Cell) RNA-seq Data

# 
# quickmart = function(genome = 'hg19',
#                      host = 'ensembl.org') {
#     if (genome == 'hg19') {
#         dataset = 'hsapiens_gene_ensembl'
#         host = "grch37.ensembl.org"
#     }
#     else if (genome == 'hg38') {
#         dataset = 'hsapiens_gene_ensembl'
#         host = "useast.ensembl.org"
#     }
#     else if (genome == 'mm10') {
#         dataset = "mmusculus_gene_ensembl"
#     }
#     else {
#         stop('genome "', genome, '" not found')
#     }
#     # Choose which species to use and server to download from
#     biomaRt::useMart("ENSEMBL_MART_ENSEMBL",
#              dataset = dataset,
#              host = host,
#              port = 80)
# }
# 
# getGenome = function(mart, add_attribute = 'hgnc_symbol') {
#     filters = c('chromosome_name', 'hgnc_symbol')
#     values = list(c(1:22, 'X', 'Y'), load('genes.rda'))
#     attributes = c('chromosome_name',
#                    'band',
#                    'strand',
#                    'start_position',
#                    'end_position')
#     attributes = unique(c(attributes, add_attribute))
#     result = biomaRt::getBM(attributes = attributes,
#                             mart = mart,
#                             filters = filters,          
#                             values = values,
#                             uniqueRows = T)
#     if ('hgnc_symbol' %in% add_attribute) {
#         result = dplyr::filter(result, hgnc_symbol != "")
#     }
#     if ('mgi_symbol' %in% add_attribute) {
#         result = dplyr::filter(result, mgi_symbol != "")
#     }
#     result
# }