Vignette Example Error

[Rosemary Luong]

Hello, I'm trying to go through the vignette example with the example files provided. I have typed out the code I used and the error I got below.

Code

install.packages("MixviR")
library (MixviR)
setwd("/Users/Username/Downloads/example_mixvir_files")
samp_mutations <- call_mutations(sample.dir = system.file("extdata", "vcfs",
                                                          package = "MixviR"),
                                 reference = "Wuhan",
                                 name.sep = "_")

Error

Error in `dplyr::mutate()`:
! Problem while computing `TYPE = dplyr::case_when(...)`.
Caused by error in `ALT2 %in% c("del", "ins", "Fdel", "Fins")`:
! object 'ALT2' not found

I would greatly appreciate any advice, thank you so much in advance!

[Mike Sovic]

Hello Rosemary,

I think you may need to install the Biostrings package from Bioconductor. It looks like it might not be getting installed as part of the CRAN installation. I'll see if I can get that fixed in the next version, but for now, if you're getting this or a similar error message when running either the example data or your actual files, try the following...

install.packages("BiocManager")

BiocManager::install("Biostrings")

Then try your example code again and let me know if you still have issues.

           Mike

[Rosemary Luong]

It works now! Thank you so much.

Rosemary