preserve indiv info read from the bed file

R/gen_tibble.R

@@ -123,6 +123,35 @@ gen_tibble_bed_rds <- function(x, ...,
                                            bigsnp_file = bigsnp_path,
                                            indiv_id = bigsnp_obj$fam$sample.ID)
 
+  # transfer some of the fam info to the metadata table if it is not missing (0 is the default missing value)
+  fam_info <- .gt_get_bigsnp(indiv_meta)$fam
+  if(!all(fam_info$paternal.id==0)){
+    indiv_meta$paternal_ID <- fam_info$paternal.id
+    indiv_meta$paternal_ID[indiv_meta$paternal_ID==0]<-NA
+  }
+  if(!all(fam_info$maternal.id==0)){
+    indiv_meta$maternal_ID <- fam_info$maternal.id
+    indiv_meta$maternal_ID[indiv_meta$maternal_ID==0]<-NA
+  }
+  if(!all(fam_info$sex==0)){
+    indiv_meta$sex <-   dplyr::case_match(
+      fam_info$sex,
+      1 ~ "male",
+      2 ~ "female",
+      .default = NA,
+      .ptype = factor(levels = c("female", "male"))
+    )
+  }
+  if(!all(fam_info$affection %in% c(0,-9))){
+  indiv_meta$phenotype <- dplyr::case_match(
+    fam_info$affection,
+    1 ~ "control",
+    2 ~ "case",
+    -9 ~ NA,
+    .default = NA,
+    .ptype = factor(levels = c("control", "case"))
+  )
+  }
   new_gen_tbl <- tibble::new_tibble(
     indiv_meta,
     class = "gen_tbl"

tests/testthat/test_gt_as_plink.R

@@ -39,9 +39,9 @@ test_that("write a bed file",{
 
   # write it as raw
   raw_path <- gt_as_plink(test_gt,file=tempfile(),type="raw")
-  # check why sex has been lost (it was not read in properly?!?)
-  # look at line 119 of gen_tibble
-  #tools::md5sum(raw_path)==tools::md5sum(system.file("extdata","pop_a.raw",package="tidypopgen"))
-
+  raw_file_test <- read.table(raw_path, header= TRUE)
+  mat <- as.matrix(raw_file_test[,7:ncol(raw_file_test)])
+  mat <- unname(mat)
+  expect_true(all.equal(mat,show_genotypes(test_gt)))
 })
 

vignettes/example_clustering_and_dapc.Rmd

@@ -3,7 +3,7 @@ title: "example workflow with tidypopgen"
 output: rmarkdown::html_vignette
         #pdf_document
 vignette: >
-  %\VignetteIndexEntry{example_workflow}
+  %\VignetteIndexEntry{example workflow with tidypopgen}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---

vignettes/overview.Rmd

@@ -367,12 +367,14 @@ write a file in the appropriate format, and return the name of that file on comp
 For example, to export to a PLINK .bed file, we simply use:
 
 ```{r}
-gt_as_plink(example_gt, bedfile =  tempfile("new_bed_"))
+gt_as_plink(example_gt, file =  tempfile("new_bed_"))
 ```
 
 This will also write a .bim and .fam file and save them together with the .bed file. 
 Note that, from the main tibble, only
 on `id`, `population` and `sex` will be preserved in the .fam file.
+It is also possible to write .ped and .raw files by specifying `type="ped"` or
+`type="raw"` in `gt_as_plink()` (see the help page for `gt_as_plink()` for details).
 
 # Merging data