Gets Gemma's platform annotations including mappings of microarray probes to genes.
A platform numerical identifiers or platform short name.
Which GO terms should the output include
Where to save the annotation file to, or empty to just load into memory
Whether or not to overwrite an existing file
Whether or not to save to cache for future calls with the
same inputs and use the result saved in cache if a result is already saved.
Doing options(gemma.memoised = TRUE) will ensure that the cache is always
used. Use forget_gemma_memoised to clear the cache.
Whether or not to unzip the file (if @param file is not empty)
A table of annotations
ElementName: Probeset names provided by the platform.
Gene symbols for generic annotations typicall used for RNA-seq experiments.
GeneSymbols: Genes that were found to be aligned to
the probe sequence. Note that it is possible for probes to be
non-specific. Alignment to multiple genes are indicated with gene
symbols separated by "|"s
GeneNames: Name of the gene
GOTerms: GO Terms associated with the genes. annotType
argument can be used to choose which terms should be included.
GemmaIDs and NCBIids: respective IDs for the genes.
head(get_platform_annotations("GPL96"))
#> java.io.OutputStreamWriter@5b760059ElementName GeneSymbols
#> <char> <char>
#> 1: 202619_s_at PLOD2
#> 2: 219952_s_at MCOLN1
#> 3: 205192_at MAP3K14
#> 4: 212724_at RND3
#> 5: 207373_at HOXD10
#> 6: 204991_s_at NF2
#> GeneNames
#> <char>
#> 1: procollagen-lysine,2-oxoglutarate 5-dioxygenase 2
#> 2: mucolipin TRP cation channel 1
#> 3: mitogen-activated protein kinase kinase kinase 14
#> 4: Rho family GTPase 3
#> 5: homeobox D10
#> 6: NF2, moesin-ezrin-radixin like (MERLIN) tumor suppressor
#> GOTerms
#> <char>
#> 1: GO:0005506|GO:0001666|GO:0030867|GO:0031418|GO:0005789|GO:0070062|GO:0033823|GO:0005783|GO:0008475|GO:0006493|GO:0046947|GO:0017185|GO:0036211
#> 2: GO:0006812|GO:0051209|GO:0005764|GO:0005765|GO:0005886|GO:0097682|GO:0042995|GO:0005261|GO:0005262|GO:0002250|GO:1901660|GO:0019722|GO:0070588|GO:0099604|GO:0051289|GO:0072345|GO:0033572|GO:0071277|GO:0005515|GO:0031902|GO:0090382|GO:0005654|GO:0097352|GO:0010008|GO:0043235|GO:0001891|GO:0005794|GO:0043231|GO:0008289|GO:0005770|GO:1905673|GO:0042802|GO:0005381|GO:0034755|GO:0030670|GO:0071467|GO:0016020|GO:0051179
#> 3: GO:0106310|GO:0005515|GO:0000165|GO:0001650|GO:0005524|GO:0006955|GO:0071260|GO:0005654|GO:0007249|GO:0038061|GO:0004672|GO:0004674|GO:0051607|GO:0043231|GO:0004709|GO:0016310|GO:0005829
#> 4: GO:0005925|GO:0005515|GO:0032956|GO:0000139|GO:0005525|GO:0005886|GO:0007015|GO:0007155|GO:0007165|GO:0007264|GO:0019901|GO:0030036|GO:0016477|GO:0005829|GO:0003924
#> 5: GO:0001228|GO:0030326|GO:0048935|GO:0003682|GO:0006357|GO:0045786|GO:0035136|GO:0035137|GO:0045944|GO:0005829|GO:0000978|GO:0036464|GO:0007519|GO:0005515|GO:0005634|GO:0021520|GO:0005654|GO:0007338|GO:0000981|GO:0000785|GO:0048704|GO:0050905|GO:0008344|GO:0009952|GO:0009954|GO:1990837|GO:0017053
#> 6: GO:0005769|GO:0005886|GO:1902966|GO:0042475|GO:0043005|GO:0044297|GO:0008285|GO:0008360|GO:0043409|GO:2000177|GO:0070306|GO:0032587|GO:0035330|GO:0005737|GO:0005856|GO:0031527|GO:0000165|GO:0031647|GO:0005730|GO:0005178|GO:0007398|GO:0045597|GO:0030036|GO:0021766|GO:0016020|GO:0048471|GO:0051726|GO:0030027|GO:0030864|GO:0042532|GO:0001707|GO:0005829|GO:0014013|GO:0022408|GO:0014010|GO:0005515|GO:0001953|GO:0005912|GO:0003779|GO:0005634|GO:0030336|GO:0045216|GO:0010626|GO:0042981|GO:0046426|GO:0072091|GO:1902115|GO:0045177|GO:1900180|GO:2000643|GO:0033689|GO:0033687|GO:0030175|GO:0032154|GO:0051496
#> GemmaIDs NCBIids EnsemblIds
#> <char> <char> <char>
#> 1: 127276 5352 ENSG00000152952
#> 2: 313978 57192 ENSG00000090674
#> 3: 188876 9020 ENSG00000006062
#> 4: 9353 390 ENSG00000115963
#> 5: 72301 3236 ENSG00000128710
#> 6: 116071 4771 ENSG00000186575
head(get_platform_annotations('Generic_human_ncbiIds'))
#> ElementName GeneSymbols
#> <int> <char>
#> 1: 55236 UBA6
#> 2: 79664 ICE2
#> 3: 100126270 FMR1-AS1
#> 4: 105373684 LINC01818
#> 5: 124900245 LOC124900245
#> 6: 102725051 LOC102725051
#> GeneNames
#> <char>
#> 1: ubiquitin like modifier activating enzyme 6
#> 2: interactor of little elongation complex ELL subunit 2
#> 3: FMR1 antisense RNA 1
#> 4: long intergenic non-protein coding RNA 1818
#> 5: small nucleolar RNA SNORA40
#> 6: uncharacterized LOC102725051
#> GOTerms
#> <char>
#> 1: GO:0005515|GO:0006511|GO:0032446|GO:0021766|GO:0019780|GO:0004792|GO:0007612|GO:0016567|GO:0005737|GO:0060996|GO:0005829|GO:0007626|GO:0005524|GO:0004839|GO:0016779|GO:0021764
#> 2: GO:0016604|GO:0005515|GO:0008023|GO:0005654|GO:0000791|GO:0045945|GO:0042795|GO:0005829|GO:0042796|GO:0015030|GO:0035363
#> 3: GO:0043066
#> 4:
#> 5:
#> 6:
#> GemmaIDs NCBIids
#> <int> <int>
#> 1: 295849 55236
#> 2: 336840 79664
#> 3: 3157248 100126270
#> 4: 9235895 105373684
#> 5: 10578422 124900245
#> 6: 9008981 102725051