The function pulls the gene ontology (GO) terms for a set of feature names.
getGOFromFeatures(
id,
namespace = "cellular_component",
evidence = NULL,
params = NULL,
verbose = FALSE,
nmax = 500
)An character with feature names to be pulled from
biomart. If and MSnSet is provided, then
featureNames(id) is used.
The GO namespace. One of
biological_process, cellular_component (default)
or molecular_function.
The GO evidence code. See
showGOEvidenceCodes for details. If NULL
(default), no filtering based on the evidence code is
performed.
An instance of class
"AnnotationParams".
A logical defining verbosity of the
function. Default is FALSE.
As described in
https://support.bioconductor.org/p/86358/, the Biomart
result can be unreliable for large queries. This argument
splits the input in chunks of length nmax (default is
500). If set to NULL, the query is performed in full.
A data.frame with relevant GO terms.
library(pRolocdata)
data(dunkley2006)
data(dunkley2006params)
dunkley2006params
#> Object of class "AnnotationParams"
#> Using the 'plants_mart' BioMart database
#> Using the 'athaliana_eg_gene' dataset
#> Using 'tair_locus' as filter
#> Created on Tue Mar 12 07:25:12 2024
fn <- featureNames(dunkley2006)[1:5]
getGOFromFeatures(fn, params = dunkley2006params)
#> tair_locus go_id namespace_1003
#> 3 AT1G09210 GO:0005783 cellular_component
#> 7 AT1G09210 GO:0005788 cellular_component
#> 9 AT1G09210 GO:0005783 cellular_component
#> 10 AT1G09210 GO:0005576 cellular_component
#> 11 AT1G09210 GO:0005739 cellular_component
#> 12 AT1G09210 GO:0099503 cellular_component
#> 14 AT1G09210 GO:0000325 cellular_component
#> 16 AT1G21750 GO:0005783 cellular_component
#> 17 AT1G21750 GO:0005634 cellular_component
#> 20 AT1G21750 GO:0005773 cellular_component
#> 21 AT1G21750 GO:0005788 cellular_component
#> 22 AT1G21750 GO:0005783 cellular_component
#> 26 AT1G21750 GO:0099503 cellular_component
#> 27 AT1G21750 GO:0009579 cellular_component
#> 29 AT1G21750 GO:0000325 cellular_component
#> 32 AT1G21750 GO:0000326 cellular_component
#> 33 AT1G21750 GO:0000327 cellular_component
#> 36 AT1G51760 GO:0005783 cellular_component
#> 37 AT1G51760 GO:0005634 cellular_component
#> 38 AT1G51760 GO:0005788 cellular_component
#> 40 AT1G51760 GO:0005783 cellular_component
#> 44 AT1G56340 GO:0005783 cellular_component
#> 48 AT1G56340 GO:0005788 cellular_component
#> 51 AT1G56340 GO:0005634 cellular_component
#> 52 AT1G56340 GO:0009506 cellular_component
#> 53 AT1G56340 GO:0005783 cellular_component
#> 54 AT1G56340 GO:0005739 cellular_component
#> 55 AT1G56340 GO:0099503 cellular_component
#> 57 AT1G56340 GO:0000325 cellular_component
#> 59 AT2G32920 GO:0005783 cellular_component
#> 61 AT2G32920 GO:0005788 cellular_component
#> 62 AT2G32920 GO:0005783 cellular_component
#> 64 AT2G32920 GO:0005794 cellular_component
#> 66 AT2G32920 GO:0000325 cellular_component
#> name_1006 go_linkage_type
#> 3 endoplasmic reticulum IEA
#> 7 endoplasmic reticulum lumen IEA
#> 9 endoplasmic reticulum HDA
#> 10 extracellular region HDA
#> 11 mitochondrion HDA
#> 12 secretory vesicle HDA
#> 14 plant-type vacuole HDA
#> 16 endoplasmic reticulum IEA
#> 17 nucleus HDA
#> 20 vacuole IEA
#> 21 endoplasmic reticulum lumen IEA
#> 22 endoplasmic reticulum HDA
#> 26 secretory vesicle HDA
#> 27 thylakoid HDA
#> 29 plant-type vacuole HDA
#> 32 protein storage vacuole IDA
#> 33 lytic vacuole within protein storage vacuole IDA
#> 36 endoplasmic reticulum IEA
#> 37 nucleus HDA
#> 38 endoplasmic reticulum lumen IEA
#> 40 endoplasmic reticulum HDA
#> 44 endoplasmic reticulum IEA
#> 48 endoplasmic reticulum lumen IEA
#> 51 nucleus HDA
#> 52 plasmodesma HDA
#> 53 endoplasmic reticulum HDA
#> 54 mitochondrion HDA
#> 55 secretory vesicle HDA
#> 57 plant-type vacuole HDA
#> 59 endoplasmic reticulum IEA
#> 61 endoplasmic reticulum lumen IEA
#> 62 endoplasmic reticulum HDA
#> 64 Golgi apparatus HDA
#> 66 plant-type vacuole HDA