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Cannot extract results from enrichPathway #21
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ibichind
changed the title
Cannot extracr results from enrichPathway
Cannot extract results from enrichPathway
Nov 12, 2018
any reproducible example? |
Yes, please find the sample file in attachment. |
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Dear GuangchuangYu,
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I have some code to analyze a dataset that I used in 2016 and that produced great results..
genes <- geneNames[bss$ix[1:100],1]
genes <- as.character(genes)
hugoNames <- lapply(genes, function(t) substr(t, 1, regexpr("\|", t) - 1)) # extract HUGO names
entrezNames <- lapply(genes, function(t) substr(t, regexpr("\|", t) + 1, nchar(t))) # extract Entrez names
paths = enrichPathway(gene=unlist(entrezNames), pvalueCutoff=.9, readable=T)
With the latest version of ReactomePA (1.26.0) and DOSE (1.38) for R 3.5.1 under Windows x64, I see that I am getting results in the 'paths' variable, but cannot extract them or visualize them - all figures are blank. See below.
head(as.data.frame(paths))
enrichMap(paths, layout=igraph::layout.kamada.kawai, vertex.label.cex = 1)
Please help. Thank you. Isabelle
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