Nothing
# Read
library(magrittr)
library(multicrispr)
bedfile <- system.file('extdata/SRF.bed', package = 'multicrispr')
gr <- bed_to_granges(bedfile, 'mm10')
# Functions
write <- function(x, file){
write.table(x, file, quote = FALSE, row.names = FALSE, col.names = FALSE)
}
# Entrez
dbname <- 'TxDb.Mmusculus.UCSC.mm10.knownGene'
db <- utils::getFromNamespace(dbname, dbname)
entrez <- annotate_granges(gr, db) %>%
magrittr::extract(!is.na(.$gene_id)) %>%
data.table::as.data.table() %>%
magrittr::extract(,
list(seqnames, start, end, strand, entrez=gene_id))
# Ensembl
db <- AnnotationHub::AnnotationHub()[["AH75036"]] #EnsDb.Mmusculus.v98
ensembl <- annotate_granges(gr, db) %>%
magrittr::extract(!is.na(.$gene_id)) %>%
data.table::as.data.table() %>%
magrittr::extract(,
list(seqnames, start, end, strand, ensembl=gene_id))
# Intersect
both <- merge(entrez, ensembl, by = c('seqnames', 'start', 'end', 'strand'))
set.seed(3)
idx <- sample(seq_len(nrow(both)), 10)
both$entrez[ idx] %>% write('inst/extdata/SRF.entrez')
both$ensembl[idx] %>% write('inst/extdata/SRF.ensembl')
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