View source: R/17_subset_allchains.R
allchains.cat | R Documentation |
Function to evaluate the specific chains enriched within each category
allchains.cat(X, Y, test = "Fisher", enrich = FALSE, pval = 0.05,
adjpval = 1, TGcollapse.rm = TRUE)
X |
has to be a <Query>.intact object that was created using the lipid.miner function |
Y |
has to be your <Universe>.intact object that was created using the lipid.miner function |
test |
has to be a type of test in the list "Fisher", "Binom", "Hyper", or "EASE" |
enrich |
TRUE or FALSE (FALSE by default) to choose between showing all the results of the test or only the enriched ones based on a pvalue |
pval |
regular pvalue cutoff (0.05 by default) |
adjpval |
BH adjusted pvalue cutoff (1.0 by default) |
TGcollapse.rm |
Boolean to indicate if the collapsed TG need to be removed (default TRUE) |
This function will return a data.frame containing the tested classifiers (rows), the counts and percentage of identifiers/chains falling in this classifier, a binom.test() pvalue, a BH corrected pvalue and a fold change
Geremy Clair
allchains.cat(queryExample.intact,universeExample.intact,test="Hyper",enrich=TRUE, p=0.05)
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