library(org.Hs.eg.db)
library(magrittr)
ls("package:org.Hs.eg.db")
keys <- head( keys(org.Hs.eg.db, keytype="SYMBOL") )
keys
keys <- "RUNX1"
keytypes(org.Hs.eg.db)
select(org.Hs.eg.db, keys=keys, columns = c("UNIPROT"),
keytype="SYMBOL")
# Ensembl
x <- org.Hs.egENSEMBL
mapped_genes <- mappedkeys(x)
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
# Get the Ensembl gene IDs for the first five genes
xx[1:5]
# Get the first one
xx[[1]]
}
head(xx)
# Ensembl Protein
x <- org.Hs.egENSEMBLPROT
# Get the entrez gene IDs that are mapped to an Ensembl ID
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
# Get the Ensembl gene IDs for the first five proteins
xx[1:5]
# Get the first one
xx[[1]]
}
head(xx)
mapped_genes <- 9606
xx <- as.list(x[mapped_genes])
edb <- EnsDb.Hsapiens.v75
supportedFilters(edb)
Tx <- transcripts(edb, filter = list(GenenameFilter("RUNX1")))
Tx
start(Tx)
Tx$tx_biotype
edb %>% filter(~ symbol == "RUNX1" & tx_biotype != "protein_coding") %>% transcripts
listTables(edb)
## Define the filter
grf <- GRangesFilter(GRanges("11", ranges = IRanges(114129278, 114129328),
strand = "+"), type = "any")
## Query genes:
gn <- genes(edb, filter = grf)
gn
txs <- transcripts(edb, filter = GenenameFilter(gn$gene_name))
txs
library(ggbio)
## Create a plot for all transcripts of the gene SKA2
autoplot(edb, ~ genename == "SKA2")
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