#' @import data.table
#' @import GenomeInfoDb
#' @import BSgenome
#' @importFrom utils .DollarNames data packageVersion download.file tail
#' @importFrom methods is new
#' @importFrom stats na.omit predict setNames dist window
.datatable.aware = TRUE
.ces_ref_data = new.env()
options(datatable.prettyprint.char = 40)
# Data package names and minimum required version
.official_refsets = list(ces.refset.hg19 = as.package_version("1.1.0"), ces.refset.hg38 = as.package_version("1.2.0"))
# If refset packages are loaded, put their data in .ces_ref_data for easy access
for(refset in names(.official_refsets)) {
if(refset %in% loadedNamespaces()) {
.ces_ref_data[[refset]] = get(refset, envir = as.environment(paste0('package:', refset)))
lockEnvironment(.ces_ref_data[[refset]], bindings = TRUE)
}
}
snv_annotation_template = data.table(variant_name = character(), snv_id = character(), chr = character(), pos = numeric(),
ref = character(), alt = character(), genes = list(), intergenic = logical(),
trinuc_mut = character(), essential_splice = logical(),
nearest_pid = list(), covered_in = list())
aac_annotation_template = data.table(variant_name = character(), aac_id = character(), gene = character(), aachange = character(),
strand = integer(), chr = character(), pid = character(), aa_ref = character(),
aa_pos = numeric(), aa_alt = character(),
nt1_pos = numeric(), nt2_pos = numeric(), nt3_pos = numeric(),
coding_seq = character(), constituent_snvs = list(), essential_splice = logical(),
covered_in = list())
aac_snv_key_template = data.table(aac_id = character(), snv_id = character(), multi_anno_site = logical(), key = 'aac_id')
sample_table_template = data.table(Unique_Patient_Identifier = character(), coverage = character(),
covered_regions = character(), sig_analysis_grp = integer(), gene_rate_grp = integer(),
maf_source = character())
# for use when identifying a column previously handled by cancereffectsizeR
# "merged_into_other_variant" replaced with "merged_with_nearby_variant" in 2.6.4
preload_problems = c('missing_values', 'not_variant', 'duplicate_record', 'failed_liftOver',
'duplicate_record_after_liftOver', 'unsupported_chr', 'out_of_bounds',
'reference_mismatch', "merged_into_dbs_variant", "merged_into_other_variant",
"duplicate_from_TCGA_sample_merge", "merged_with_nearby_variant", "invalid_record")
# format a string the way R should automatically, then feed it to message()
pretty_message = function(msg, emit = T, black = emit) {
msg = paste0(strwrap(msg), collapse = "\n")
if (black) {
# If current theme is dark, make the message white
if(Sys.getenv("RSTUDIO") == "1" && rstudioapi::isAvailable() && rstudioapi::getThemeInfo()$dark) {
msg = crayon::white(msg) # nocov
} else {
msg = crayon::black(msg)
}
}
if (emit) {
message(msg)
} else {
return(msg)
}
}
NULL
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