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caitiecollins / treeWAS

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
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Error in treeWAS(snps = snps, phen = phen, tree = tree, n.subs = NULL, : Some elements of tree$tip.label are absent from names(phen). #70

Open xqzangnolan opened 1 year ago

xqzangnolan commented 1 year ago

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 commented 1 year ago

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 caitiecollins@gmail.com.

Best, Caitlin.