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Interaction with other annotation libraries for GO #3

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oganm opened this issue Jan 31, 2018 · 3 comments
Closed

Interaction with other annotation libraries for GO #3

oganm opened this issue Jan 31, 2018 · 3 comments

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oganm commented Jan 31, 2018

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oganm commented Feb 27, 2018 •
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biomart godb biomartr

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oganm commented Feb 27, 2018

go enrichment packages, gostats, GOexpress, toGO, ...

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oganm commented Feb 28, 2018 •
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goStats doesn't have a way of getting go terms. in example it gets it from the array db package. topGo also does the same. A pipeline is

affyLib = paste0(annotation(ExpressionSetObject), '.db')
library(package = affyLib, character.only = TRUE)
goTerms = as.list(eval(parse(text = paste0(annotation(ExpressionSetObject) ,'GO'))))

propagating go terms

as.list(GO.db::GOBPANCESTOR)

@oganm oganm closed this as completed Mar 2, 2018
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