#========= Load default paths on package load =========#
.onLoad <- function(libname, pkgname){
## Java
assign('JAVA_PATH', system('which java',intern=T), envir=parent.env(environment()))
## Paths within the package
pkg_constant_paths <- list(
c('SNPSIFT_PATH','../dep/snpEff/SnpSift.jar'),
c('SNPEFF_PATH','../dep/snpEff/snpEff.jar'), ## snpEff has requires databases that are downloaded to ./ the first time
c('BED_FILE','misc/cosmic_cancer_gene_census_20200225.bed'),
c('EXONS_BED_FILE','misc/cosmic_cancer_gene_census_exons_20200225.bed.gz'),
c('CENTROMERE_POSITIONS','db/centromere_positions_hg19.txt'),
c('GENES_ENST2ENSG','db/human_genes_enst2ensg.txt.gz'),
c('GENES_HGNC','db/hgnc_gene_names.txt.gz'),
c('CLINVAR_PATH','db/clinvar.txt.bgz')
)
for(i in pkg_constant_paths){
assign( i[1], system.file(i[2], package='hmfGeneAnnotation'), envir=parent.env(environment()) )
}
## Load clinvar and snpeff scoring tables
scoring_txt_files <- list(clinvar='scoring/clinvar_scoring.txt',snpeff='scoring/snpeff_scoring.txt')
scoring_txt_files <- lapply(scoring_txt_files, function(i){ system.file(i,package='hmfGeneAnnotation') })
SCORING_MUT <- lapply(scoring_txt_files, function(i){
df <- read.delim(i, stringsAsFactors=F)
structure(df$score, names=df$annotation)
})
assign('SCORING_MUT', SCORING_MUT, envir=parent.env(environment()))
}
ONE_ARMED_CHROMS <- c(13,14,15,21,22)
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