fbaumdicker / aimsetfinder Goto Github PK

We have recently learned that there was an error in the description of the Gutenkunst et al model provided as an example in the msprime tutorial. It appears that you are using a copy of the incorrect model in this repo, and so I am opening this issue to alert you.

Please see here for details on what the error is, and what actions you can take to fix it.

We have also written a short note analysing this and another related error, detailing the likely effects on downstream analysis. Thankfully, the differences between the misspecified model from msprime's documentation and the intended model are slight.

I apologise for this error and I sincerely hope that it has not affected your research.

In the How to run section of the README you have example_pipeline.r where it should say pipeline_example.r. There also a couple of LaTeX bits in the README that could do with tidying up.

For an input VCF containing a single variant and multiple samples, the getData method in tools.r fails with the error message below. I encounter this problem when trying to carry out step5 of the pipeline_1000G_AIMs_noAMR.r script applied to a reduced set of variants.

Error in rownames<-(x, value) : attempt to set 'rownames' on an object with no dimensions Calls: getData -> row.names<- -> row.names<-.default -> rownames<- Execution halted