Error in treeWAS(snps = snps, phen = phen, tree = tree, n.subs = NULL, : Some elements of tree$tip.label are absent from names(phen).

[xqzangnolan]

excuse me,
when I run "
out <- treeWAS(snps = snps,
phen = phen,
tree = tree,
n.subs = NULL, ## (optional input: n.subs)
n.snps.sim = ncol(snps)*10,
chunk.size = ncol(snps),
test = c("terminal", "simultaneous", "subsequent"),
snps.reconstruction = "parsimony", ## (optional input: snps.rec)
snps.sim.reconstruction = "parsimony",
phen.reconstruction = "parsimony",
phen.type = NULL,
na.rm = TRUE,
p.value = 0.01,
p.value.correct = "bonf",
p.value.by = "count",
dist.dna.model = "JC69",
plot.tree = TRUE,
plot.manhattan = TRUE,
plot.null.dist = TRUE,
plot.dist = FALSE,
snps.assoc = NULL,
filename.plot = NULL,
seed = 1)"

the followed sentences returned" Error in treeWAS(snps = snps, phen = phen, tree = tree, n.subs = NULL, :
Some elements of tree$tip.label
are absent from names(phen)."
But I checked the tree$tip.label was the same as the names(phen).

Looking forward to your help,
Best,
Xiaoqi

[caitiecollins]

Hi,

Could you please confirm by running this line on your tree and phen:
all(tree$tip.label %in% names(phen))

Does it return TRUE?

If you are able to share your tree and phen data with me, I'm also happy to take a look and figure out what's going on. You could attach your data publicly here or send it to me privately at [email protected].

Best,
Caitlin.