treeWAS

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long vectors not supported yet

3

Hi Caitlin, Thanks for developing TreeWAS! I'm trying to use unitigs with TreeWAS, and have been running into the below error: ``` Error in unlist(snps[!is.na(snps)]) : long vectors not supported...

daisy238

When I successfully run the treeWAS, but some Note and Warning for me..... Reconstruction type must be 'ML' when variable is 'continuous'. Setting type to 'ML'. Note: Updating n.snps.sim to...

allanlinzhang

allanlinzhang

Hi, could you recommend a tool or script to know the calculated significant snp related to which gene? (your paper PLOS ComputationalBiology |https:/ /doi.org/10.1371/journal.pcbi.1005958, table 2). Looking forward to your...

xqzangnolan

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

1

excuse me, when I run " out

xqzangnolan

Hi Caitie, I am using treeWAS in this dataset of 3000-4000 samples and 229626 unitigs. I kept running into memory error even after I adjusted the chunk size (I have...

DorothyTamYiLing

Hi Caitie, When I try to run the demo dataset as shown in vignette, I came across an error `Error in ncol(snps.ori) : object 'snps.ori' not found` . The same...

jiyekwon

Ancestral state reconstruction with phytools

2

Hi Caitie, What I write here is more of a doubt than an error, which I hope you can help me solve. I am currently using your software and I...

ruutmdlv

input data

5

Hello, I want to use treeWAS for Bacterial GWAS, and my data is in the form of SNPs and gene presence /absence, but when I run the program I get...

mohammadzarrabian

Hello, I am still new to treeWAS, so maybe this is a silly question. I am considering using output from ClonalFrameML. I have a question: will the significant SNPs/positions found...

Angelika-2Z-Borowiecka