src_organism {Organism.dplyr} | R Documentation |
The database provides a convenient way to map between gene, transcript, and protein identifiers.
src_organism(txdb = NULL, dbpath = NULL) src_ucsc(organism, genome = NULL, id = NULL, dbpath = NULL, verbose = TRUE) supportedOrganisms() ## S3 method for class 'tbl_organism' select_(.data, ...) ## S3 method for class 'src_organism' src_tbls(x) ## S3 method for class 'src_organism' tbl(src, ..., .load_tbl_only = FALSE) ## S4 method for signature 'src_organism' orgPackageName(x) ## S4 method for signature 'src_organism' seqinfo(x)
txdb |
character(1) naming a |
dbpath |
path and file name where SQLite file will be accessed or created if not already exists. |
organism |
organism or common name |
genome |
genome name |
id |
choose from "knownGene", "ensGene" and "refGene" |
verbose |
logical. Should R report extra information on progress? Default is TRUE. |
.data |
A tbl. |
... |
Comma separated list of unquoted expressions. You can treat variable names like they are positions. Use positive values to select variables; use negative values to drop variables. |
x |
A src_organism object |
src |
An src_organism object |
.load_tbl_only |
a logic(1) that indicates whether only to load the table instead of also loading the pacakge in the temporary database. Default value is FALSE. |
src_organism()
and src_ucsc()
are meant to be a building block
for src_organism
, which provides an integrated
presentation of identifiers and genomic coordinates.
src_organism()
creates a dplyr database integrating org.* and TxDb.*
information by given TxDb. And src_ucsc()
creates the database by
given organism name, genome and/or id.
supportedOrganisms() provides all supported organisms in this package with corresponding OrgDb and TxDb.
src_organism()
and src_ucsc()
returns a dplyr
src_dbi
instance representing the data tables.
A tbl_df of the requested table coming from the temporary database of the src_organism object.
Yubo Cheng.
dplyr
for details about using dplyr
to
manipulate data.
transcripts_tbl
for generic functions to
extract genomic features from a src_organism
object.
select,src_organism-method
for "select"
interface on src_organism
objects.
## create human sqlite database with TxDb.Hsapiens.UCSC.hg38.knownGene and ## corresponding org.Hs.eg.db ## Not run: src <- src_organism("TxDb.Hsapiens.UCSC.hg38.knownGene") src <- src_organism(dbpath=hg38light()) ## query using dplyr inner_join(tbl(src, "id"), tbl(src, "id_go")) %>% filter(symbol == "ADA") %>% dplyr::select(entrez, ensembl, symbol, go, evidence, ontology) ## create human sqlite database using hg38 genome ## Not run: human <- src_ucsc("human") ## all supported organisms with corresponding OrgDb and TxDb supportedOrganisms() ## Look at all available tables src_tbls(src) ## Look at data in table "id" tbl(src, "id") ## Look at fields of one table colnames(tbl(src, "id")) ## name of org package of src_organism object orgPackageName(src) ## seqinfo of src_organism object seqinfo(src)