This function is the umbrella function for the hpaXml function family. It
take the input of either one Ensembl gene id or a imported XML object
resulting from a hpaXmlGet() function call. By default, it will
extract all information available for HPAanalyze user from the XML file by
calling every hpaXml function and put all results into a list.
hpaXml(
inputXml,
extractType = c("ProtClass", "TissueExprSum", "Antibody", "TissueExpr"),
...
)Input can be either one Ensembl gene id (start with ENSG) or
a imported XML object resulting from a hpaXmlGet() function call.
You can also use HGNC gene symbol and it will be converted to ensembl id.
A vector of strings indicate which information is desired
for extraction. By default this function will call all hpaXml
functions available. Other options are 'ProtClass',
'TissueExprSum', 'Antibody', 'TissueExpr'.
Additional arguments to be passed downstream to other hpaXml functions being called behind the scene. See help files of other hpaXml functions for more information.
This function returns a list. Each element of the list is information extracted from the XML file specified using other hpaXml functions. See help file for each XML function for more information.
Other xml functions:
hpaXmlAntibody(),
hpaXmlGet(),
hpaXmlProtClass(),
hpaXmlTissueExprSum(),
hpaXmlTissueExpr()
hpaXml(inputXml='ENSG00000131979', extractType=c('ProtClass', 'TissueExprSum', 'Antibody'))
#> $ProtClass
#> # A tibble: 17 x 4
#> source id parent_id name
#> <chr> <chr> <chr> <chr>
#> 1 NA Ez NA Enzymes
#> 2 ENZYME Ec Ez ENZYME proteins
#> 3 ENZYME Eh Ec Hydrolases
#> 4 Metabolic Atlas Mp NA Metabolic proteins
#> 5 HPA Za NA Predicted intracellular proteins
#> 6 HPA Zm Za Intracellular proteins predicted by MDM and ~
#> 7 UniProt Dr NA Disease related genes
#> 8 HPA Pd NA Potential drug targets
#> 9 KEGG Ha NA Human disease related genes
#> 10 KEGG Hd Ha Congenital disorders of metabolism
#> 11 KEGG Hd4 Hd Congenital disorders of amino acid metabolism
#> 12 KEGG Hk Ha Nervous system diseases
#> 13 KEGG Hk5 Hk Other nervous and sensory system diseases
#> 14 UniProt Ua NA UniProt - Evidence at protein level
#> 15 neXtProt Nx NA Mapped to neXtProt
#> 16 neXtProt Na Nx neXtProt - Evidence at protein level
#> 17 Kim et al 2014 Ea NA Protein evidence (Kim et al 2014)
#>
#> $TissueExprSum
#> $TissueExprSum$summary
#> [1] "Cytoplasmic and nuclear expression in several tissues, most abundant in basal cells of squamous epithelia."
#>
#> $TissueExprSum$img
#> # A tibble: 7 x 2
#> tissue imageUrl
#> <chr> <chr>
#> 1 Liver http://images.proteinatlas.org/28612/64078_A_8_4_rna_selected~
#> 2 Colon http://images.proteinatlas.org/28612/64078_A_7_3_rna_selected~
#> 3 Kidney http://images.proteinatlas.org/28612/64078_A_7_5_rna_selected~
#> 4 Testis http://images.proteinatlas.org/28612/64078_A_4_6_rna_selected~
#> 5 Lymph node http://images.proteinatlas.org/28612/64078_A_8_8_rna_selected~
#> 6 Cerebral cortex http://images.proteinatlas.org/28612/64078_B_8_5_rna_selected~
#> 7 Vagina http://images.proteinatlas.org/28612/64078_B_2_2_rna_selected~
#>
#>
#> $Antibody
#> # A tibble: 1 x 4
#> id releaseVersion releaseDate RRID
#> <chr> <chr> <chr> <chr>
#> 1 HPA028612 6.0 2010-03-26 AB_10602135
#>