radiator 1.2.9 2024-01-25

Bug fix stemming from genalex files and genind conversion

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: radiator
 Type: Package
 Title: RADseq Data Exploration, Manipulation and Visualization using R
-Version: 1.2.8
-Date: 2023-04-03
+Version: 1.2.9
+Date: 2024-01-25
 Encoding: UTF-8
 Authors@R: c(
   person("Thierry", "Gosselin", email = "[email protected]", role = c("aut", "cre")),

NEWS.md

@@ -1,3 +1,8 @@
+# radiator 1.2.9 2024-01-25
+
+* Bug fix stemming from genalex files and genind conversion
+
+
 # radiator 1.2.8 2023-04-03
 
 * Several bug fix while reading VCF from ipyrad

R/gds.R

@@ -115,6 +115,28 @@ radiator_gds <- function(
 
   # check <- markers.meta$MARKERS
   # generate all the markers metadata
+
+
+    # test <- markers.meta  %>%
+  #   dplyr::distinct(MARKERS, .keep_all = TRUE) %>%
+  #   separate_markers(
+  #     data = .,
+  #     sep = "__",
+  #     markers.meta.all.only = TRUE,
+  #     biallelic = TRUE,
+  #     verbose = verbose)
+
+  # data.bk <- data
+  # data <- data.bk
+  # data <- markers.meta  %>%
+  #   dplyr::distinct(MARKERS, .keep_all = TRUE)
+  # sep = "__"
+  # markers.meta.all.only = TRUE
+  # markers.meta.lists.only = FALSE
+  # biallelic = TRUE
+  # generate.ref.alt = FALSE
+  # parallel.core = parallel::detectCores() - 1
+
   markers.meta  %<>%
     dplyr::distinct(MARKERS, .keep_all = TRUE) %>%
     separate_markers(

R/genind.R

@@ -141,12 +141,6 @@ tidy_genind <- function(
       alt.alleles %<>% dplyr::filter(REF == "ALT") %$% MARKERS_ALLELES
       if (length(alt.alleles) != n.snp) rlang::abort("Contact author problem with tidying the genind")
 
-      # test1 <- tibble::as_tibble(t(data@tab), rownames = "MARKERS") %>%
-      #   dplyr::filter(MARKERS %in% alt.alleles) %>%
-      #   dplyr::arrange(MARKERS)
-      # test2 <- tibble::as_tibble(t(data@tab[, alt.alleles]), rownames = "MARKERS") %>% dplyr::arrange(MARKERS)
-      # test3 <- tibble::as_tibble(t(data@tab[, seq(2, length(markers.meta), by = 2)]), rownames = "MARKERS") %>% dplyr::arrange(MARKERS)
-
       data <- tibble::as_tibble(t(data@tab), rownames = "MARKERS") %>%
         dplyr::filter(MARKERS %in% alt.alleles) %>%
         dplyr::mutate(
@@ -174,12 +168,12 @@ tidy_genind <- function(
 
       data <- radiator::rad_long(
         x = data,
-        cols = "MARKERS",
+        cols = c("MARKERS", "VARIANT_ID"),
         names_to = "INDIVIDUALS",
         values_to = "GT_BIN"
       ) %>%
         dplyr::left_join(strata, by = "INDIVIDUALS") %>%
-        dplyr::left_join(markers.meta, by = "MARKERS") %>%
+        dplyr::left_join(markers.meta, by = c("MARKERS", "VARIANT_ID")) %>%
         dplyr::mutate(
           INDIVIDUALS = radiator::clean_ind_names(INDIVIDUALS),
           STRATA = radiator::clean_pop_names(STRATA)

R/utils.R

@@ -367,7 +367,8 @@ generate_markers_metadata <- function(
     }
 
     if (!tibble::has_name(markers.meta, "POS")) {
-      markers.meta %<>% dplyr::mutate(CHROM = rep(1L, n.markers))
+      # markers.meta %<>% dplyr::mutate(CHROM = rep(1L, n.markers)) # error 20240125?
+      markers.meta %<>% dplyr::mutate(POS = MARKERS)
       if (verbose) message("POS info missing: dataset filled with MARKERS column")
     }
 

README.md

@@ -7,8 +7,8 @@ state and is being actively
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
 [![minimal R
 version](https://img.shields.io/badge/R%3E%3D-NA-6666ff.svg)](https://cran.r-project.org/)
-[![packageversion](https://img.shields.io/badge/Package%20version-1.2.8-orange.svg)](commits/master)
-[![Last-changedate](https://img.shields.io/badge/last%20change-2023--04--03-brightgreen.svg)](/commits/master)
+[![packageversion](https://img.shields.io/badge/Package%20version-1.2.9-orange.svg)](commits/master)
+[![Last-changedate](https://img.shields.io/badge/last%20change-2024--01--25-brightgreen.svg)](/commits/master)
 [![R-CMD-check](https://github.com/thierrygosselin/radiator/workflows/R-CMD-check/badge.svg)](https://github.com/thierrygosselin/radiator/actions)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3687060.svg)](https://doi.org/10.5281/zenodo.3687060)
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