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converting p.adjust in enrichResult
Apologize if this is asked before, I tried to search but cannot find similar issue.
Is there a way to convert the p.adjust in enrichResult to -log10(p.adjust)?
I am trying to plot the log10 p.adjust using dotplot.
I tried the following but it doesn't work:
library(DOSE)
data(geneList)
de <- names(geneList)[abs(geneList) > 2]
edo <- enrichDGN(de)
edo$p.adjust = -log10(edo$p.adjust)
Error in `$<-`(`*tmp*`, p.adjust, value = c(6.80458428978122, 5.51727026405766, :
no method for assigning subsets of this S4 class
I was able to convert to log10 and named it log10.p.adjust using mutate but then I wasn't able to do dotplot:
edo <- mutate(edo, log10.p.adjust = -log10(as.numeric(p.adjust)))
dotplot(edo,color=log10.p.adjust)
Error in match.arg(color, c("pvalue", "p.adjust", "qvalue")) :
'arg' should be one of “pvalue”, “p.adjust”, “qvalue”
Thank you in advance for your help