Hello,

I am trying to run the example data set and receive an error. The error message as is follows Error: $ operator is invalid for atomic vectors when running plotAlleleFreq. I have added the code, output, and session info to help with diagnosing the issue.

Please let me know how to proceed.

Thanks

Benjamin

Below is the code:
library(ABHgenotypeR) genotypes <- readABHgenotypes(system.file("extdata", "preprefall025TestData.csv", package = "ABHgenotypeR"), nameA = "NB", nameB = "OL") plotAlleleFreq(genos = "genotypes") sessionInfo()

Below is the output:

library(ABHgenotypeR)
genotypes <- readABHgenotypes(system.file("extdata",

•                                       "preprefall025TestData.csv",
  

•                                       package = "ABHgenotypeR"),
  

•                           nameA = "NB", nameB = "OL")
  

plotAlleleFreq(genos = "genotypes")
Error in genos$marker_names : $ operator is invalid for atomic vectors
sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] ABHgenotypeR_1.0.1

loaded via a namespace (and not attached):
[1] colorspace_1.3-2 scales_0.5.0 compiler_3.4.3 lazyeval_0.2.1 plyr_1.8.4 tools_3.4.3 pillar_1.1.0 gtable_0.2.0 tibble_1.4.2
[10] yaml_2.1.16 Rcpp_0.12.15 ggplot2_2.2.1 grid_3.4.3 rlang_0.1.6 munsell_0.4.3

plotGenos(genotypes)
Error in grid.Call.graphics(C_upviewport, as.integer(n)) :
cannot pop the top-level viewport ('grid' and 'graphics' output mixed?)
In addition: Warning message:
The panel.margin argument of theme() is deprecated as of ggplot2 2.2.0.
ℹ Please use the panel.spacing argument instead.
ℹ The deprecated feature was likely used in the ABHgenotypeR package.
Please report the issue to the authors.
This warning is displayed once every 8 hours.
Call lifecycle::last_lifecycle_warnings() to see where this warning was generated.

Dear Stefan,

I try to use your function to impute a map object created with ASMap.

when excuting the imputation, i get following error:

postImpGenotypes <- imputeByFlanks(genotypes)
Error in 1:nrow(geno_temp) : argument of length 0

Could you help me with that?
Thank you,
Michel

Trying to read in a file which contains contigs in which all SNPs are NA will result in failure. Please remove those contigs from your data prior to reading in data.