Hi there, I'm trying to run ZicoSeq on my 16S rRNA data processed with the DADA2 pipeline, but every time it tries to fit the beta mixture I get the following error message:

Fitting beta mixture ... Error in rbeta(sample.no * post.sample.no, shape1 = x + res$shape1.1, : object 'res' not found

I've tried playing around with my input table and metadata, changed the filter parameters etc. but nothing seems to be working. The function does work on the example throat data. The dimensions of my unfiltered ASV table compared to the example data are as follows:

My unfiltered ASV table:

int [1:6016, 1:133] 57254 1903 119 11683 39 14 0 0 0 43 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:6016] "TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATA"| __truncated__ "TGGGGAATATTGCACAATGGGGGGAACCCTGATGCAGCAACGCCGCGTGAAGGAAGAAGTATTTCGGTATGTAAACTTCTATCGATAGGGAAGAAAAAAATGACGGTACCT"| __truncated__ "TGGGGAATATTGCACAATGGGGGGAACCCTGATGCAGCAACGCCGCGTGAAGGAAGAAGTATTTCGGTATGTAAACTTCTATCAGCAGGGAAGAAAAAAATGACGGTACCT"| __truncated__ "TGGGGAATATTGCACAATGGGGGGAACCCTGATGCAGCAACGCCGCGTGAAGGAAGAAGTATTTCGGTATGTAAACTTCTATCGATAGGGAAGAAACAAATGACGGTACCT"| __truncated__ ...
  ..$ : chr [1:133] "ADELAIDE" "Alice" "Aparima" "Arab1" ...

Example OTU table:

int [1:856, 1:60] 1 0 0 0 0 0 0 0 0 0 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:856] "4695" "2983" "2554" "3315" ...
  ..$ : chr [1:60] "ESC_1.1_OPL" "ESC_1.3_OPL" "ESC_1.4_OPL" "ESC_1.5_OPL" ...

Any help would be greatly appreciated!

After running:
ZicoSeq.obj <- ZicoSeq(meta.dat = meta.dat3, feature.dat = comm2,
grp.name = 'CancerStatus', feature.dat.type = "count",
# Filter to remove rare taxa
prev.filter = 0.2, mean.abund.filter = 0,
max.abund.filter = 0.002, min.prop = 0,
# Winsorization to replace outliers
is.winsor = TRUE, outlier.pct = 0.03, winsor.end = 'top',
# Posterior sampling
is.post.sample = TRUE, post.sample.no = 25,
# Use the square-root transformation
link.func = list(function (x) x^0.5), stats.combine.func = max,
# Permutation-based multiple testing correction
perm.no = 99, strata = NULL,
# Reference-based multiple stage normalization
ref.pct = 0.5, stage.no = 6, excl.pct = 0.2,
# Family-wise error rate control
is.fwer = TRUE, verbose = TRUE, return.feature.dat = TRUE)

I am getting:
NA features are filtered!
Error in if (sum(!ind) != 0) { : missing value where TRUE/FALSE needed

How do I fix this?

Hello. I am having problems with the ZicoSeq.plot() function. I am runing Example.R and it works fine. But when I try to plot, I get this error:

ZicoSeq.plot(ZicoSeq.obj, meta.dat, pvalue.type = 'p.adj.fdr', cutoff = 0.1, text.size = 10,

•          out.dir = NULL, width = 10, height = 6)
  

Error in if (ZicoSeq.obj$call$feature.dat.type == "proportion") { :
argument is of length zero

I have already added the line "return.feature.dat = T" in the ZicoSeq() function, but the problem persist.

Thank you

I tested it according to the built-in data of the GUniFrac package, and it ran successfully. Then when I used my own data to run the ZicoSeq() function, it also ran successfully, but when I used ZicoSeq.plot() to draw the picture, it showed "Error in ggtitle (title.name) : object 'title.name' not found". I am thinking that the corresponding title.name parameter is not given in this ZicoSeq.plot() function, how can I solve this problem. Thanks