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