## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#",
  fig.path = "figures/",
  fig.height = 4.5, 
  fig.width = 6 
)

## ----setup, eval = FALSE------------------------------------------------------
# # Attempt to load a package, if the package was not available, install and load
# if(!require("diemr", character.only = TRUE)){
#     install.packages("diemr", dependencies = TRUE)
#     library("diemr", character.only = TRUE)
# }

## ----eval = FALSE-------------------------------------------------------------
# # Path to the vcf file
# inputfile <- system.file("extdata", "myotis.vcf", package = "diemr")
# # File name for the output
# # If working directory does not have writing privileges, the filename must include a path to a suitable folder
# outputfile <- "myotis"
# # Convert the vcf file to two diem files
# vcf2diem(SNP = inputfile, filename = outputfile, chunk = 2)
# # Expecting to include 11 markers per diem file.
# # If you expect more markers in the file, provide suitable chunk size.
# # Done with chunk 1

## ----eval = FALSE-------------------------------------------------------------
# 5 8
# ind1   AACCTTGG
# ind2   TACGATGG
# ind3   TACC-TGT
# ind4   CACGTTGG
# ind5   AACCTTGT

## ----eval = FALSE-------------------------------------------------------------
# Marker1   022_0
# Marker4   02020
# Marker5   02_00
# Marker8   00202

## ----eval = FALSE-------------------------------------------------------------
# S022_0
# S02020
# S02_00
# S00202

## ----eval = FALSE-------------------------------------------------------------
# # Import the first converted file for all individuals
# # and without changing marker polarity
# myotis <- importPolarized("myotis-01.txt",
#                           changePolarity = rep(FALSE, 11),
#                           ChosenInds = 1:14)
# # Check whether a marker includes heterozygotes
# # or that there is more than one genotype
# apply(myotis, MARGIN = 2,
#       FUN = \(x) any(grepl("1", x)) | sum(levels(factor(x)) %in% c("0", "1", "2")) > 1)
# #    m1    m2    m3    m4    m5    m6    m7    m8    m9   m10   m11
# # FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
# 

