keys can be used together to
extract data from a
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## S4 method for signature 'src_organism' keytypes(x) ## S4 method for signature 'src_organism' columns(x) ## S4 method for signature 'src_organism' keys(x, keytype, ...) select_tbl(x, keys, columns, keytype) ## S4 method for signature 'src_organism' select(x, keys, columns, keytype) ## S4 method for signature 'src_organism' mapIds(x, keys, column, keytype, ..., multiVals)
specifies the kind of keys that will be returned. By
default keys will return the keys for schema of the
other arguments. These include:
pattern: the pattern to match.
column: the column to search on.
fuzzy: TRUE or FALSE value. Use fuzzy matching? (this is used with pattern)
the keys to select records for from the database. All possible
keys are returned by using the
the columns or kinds of things that can be retrieved
from the database. As with keys, all possible columns are
returned by using the
character(1) the column to search on, can only have a single element for the value
first: when there are multiple matches only the 1st thing that comes back will be returned. This is the default behavior.
list: return a list object to the end user
filter: remove all elements that contain multiple matches and will therefore return a shorter vector than what came in whenever some of the keys match more than one value
asNA: return an NA value whenever there are multiple matches
CharacterList: returns a SimpleCharacterList object
FUN: can also supply a function to the multiVals argument for custom
behaviors. The function must take a single argument and return a
single value. This function will be applied to all the elements
and will serve a 'rule' that for which thing to keep when there
is more than one element. So for example this example function
will always grab the last element in each result:
keytypes(): discover which keytypes can be passed to keytype
argument of methods
keys(): returns keys for the
src_organism object. By default
it returns the primary keys for the database, and returns the keys from
that keytype when the keytype argument is used.
columns(): discover which kinds of data can be returned for the
select(): retrieves the data as a
tibble based on parameters
for selected keys columns and keytype arguments. If requested columns
that have multiple matches for the keys, 'select()' will return a
tibble with one row for each possible match.
mapIds(): gets the mapped ids (column) for a set of keys that are of
a particular keytype. Usually returned as a named character vector.
returns a character vector of possible values.
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## Not run: src <- src_organism("TxDb.Hsapiens.UCSC.hg38.knownGene") src <- src_organism(dbpath=hg38light()) ## keytypes keytypes(src) ## columns columns(src) ## keys keys(src, "entrez") keytype <- "symbol" keys <- c("ADA", "NAT2") columns <- c("entrez", "tx_id", "tx_name","exon_id") ## select select_tbl(src, keys, columns, keytype) select(src, keys, columns, keytype) ## mapIds mapIds(src, keys, column = "tx_name", keytype)
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