testDAA {reconsi} | R Documentation |
A function to test for differential absolute abundance on a phyloseq object
testDAA(Y, ...) ## S4 method for signature 'phyloseq' testDAA(Y, groupName, FCname, ...) ## S4 method for signature 'matrix' testDAA(Y, FC, x, S = rowSums(Y), tieBreakRan = TRUE, ...)
Y |
A phyloseq object, or a data matrix with samples in the rows and OTUs in the columns |
... |
passed on to the reconsi() function |
groupName |
A character string, the name of a variable in physeq indicating the grouping factor |
FCname |
A character string, the name of a variable in physeq containing the total cell count |
FC |
a vector of length n with total flow cytometry cell counts |
x |
a grouping factor of length n |
S |
a vector of library sizes. Will be calculated if not provided |
tieBreakRan |
A boolean, should ties be broken at random. |
See the reconsi() function
#Test for phyloseq object library(phyloseq) VandeputtePruned = prune_samples(Vandeputte, samples = sample_names(Vandeputte)[20:40]) testVanDePutte = testDAA(VandeputtePruned, "Health.status", "absCountFrozen", B = 15) #Test for matrix testMat = testDAA(as(otu_table(VandeputtePruned), "matrix"), get_variable(VandeputtePruned, "Health.status"), get_variable(VandeputtePruned,"absCountFrozen"), B = 15)