Closed aford29 closed 5 years ago
Sorry for the long delay, this issues completely escaped me. Will check the problem over the weekend
Best Thierry
genepop file need to end with .gen
So if you change that with sample_run, the codes below should work. Reopen the issue if you still have a problem...
# make sure you work with latest releases:
devtools::install_github("thierrygosselin/radiator")
devtools::install_github("thierrygosselin/assigner")
assigner::install_gsi_sim(fromSource = TRUE)
library(assigner)
data <- radiator::tidy_genomic_data(data = "sample_run.gen")
test1 <- assigner::assignment_ngs(
data = data,
assignment.analysis = "gsi_sim",
sampling.method = "ranked",
thl = 0.5)
fig <- test1$plot.assignment +
ggplot2::facet_grid(SUBSAMPLE~CURRENT) +
ggplot2::scale_y_continuous(limits = c(0,100))
fig
This should work
Hi there,
I am new to assignment analysis and found your package straight forward and somewhat easy to use. I have a panel of SNP information in genepop format and everytime I run the assignment_ngs() function I get the following error:
Tidy genomic data: Number of markers: 12 Number of chromosome/contig/scaffold: no chromosome info Number of individuals: 294 Number of populations: 5 Subsampling: selected Analyzing subsample: 1 Conducting Assignment analysis with ranked markers Using thl method, ranking Fst with training samples... Holdout samples saved in your folder Starting parallel computations for the assignment analysis: ranked markers For progress: monitor activity in the folder... | | 0%, ETA NA Compiling results Error in bindrows(x, .id) : Argument 1 must have names In addition: Warning messages: 1: In dir.create(file.path(directory)) : '/Users/aford29/Downloads/Vivax12' already exists 2: In .assigner_parallel(X = iterations.list, FUN = assignment_ranking, : scheduled cores encountered errors in user code
The warnings at the end just started happening, but the "Error in bindrows(x, .id):" has been occurring for every file that I've tried. I've also tried other files and sample files with the same error. If it helps I attached a sample of the file that I am working with
sample_run.txt
I'm not sure if it is the file that is giving me the trouble (maybe formatting errors) but I compared them with others that seemed to work and formatting wise everything seemed pretty much the same. I thought maybe using the strata function would work, but the function individuals2strata didn't work out as I may have to make one from scratch. Sorry if it seems my question/issue is all over the place; I'm pretty new to the field.
Any help you can provide would be much appreciated.