Description Usage Arguments Value Author(s) Examples
Given a list of genes associated to diseases and a background list, it calculates the diseases enrichment. It calculates both pvalues from proportion test and Fisher's exact test. Adjusted BH pvalues are returned.
1 | Enrichment(Background, Genes2Dis = g2d$clean, Genes)
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Background |
The background list of genes. In generela is the list of genes expressed. |
Genes2Dis |
A data.frame with the Gene names and the Diseases. The package has two inbuild lists. g2d_clean and g2d_complete. Both lists contains data from 4 publications (GS2D, DisGeNET, Berto2016 and PsyGeNET), however in the clean similar names were treated as the same disease. |
Genes |
A list of genes to test for enrichment |
a list contating the enrichment of diseases
Deisy Morselli Gysi <deisy at bioinf.uni-leipzig.de>
1 2 3 4 5 6 7 8 9 10 | data('g2d')
g2d_clean = g2d$clean
# The user can choose a particular disorder, or use the whole disease set to compare to
g2d_ASD = subset(g2d_clean, g2d_clean$Disease %in% c('AUTISM'))
Enrichment(Background = g2d_clean$Gene.symbol,
Genes2Dis = g2d_ASD,
Genes = g2d_ASD$Gene.symbol[1:100])
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