# radiator v.0.0.15 2018-08-17

* `genomic_converter`, `tidy_genomic_data`: bug fix when individuals are integers
* `fis_summary`: arguments updated

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: radiator
 Type: Package
 Title: RADseq Data Exploration, Manipulation and Visualization using R
-Version: 0.0.14
-Date: 2018-08-04
+Version: 0.0.15
+Date: 2018-08-17
 Encoding: UTF-8
 Authors@R: c(
   person("Thierry", "Gosselin", email = "[email protected]", role = c("aut", "cre")),

NEWS.md

@@ -1,3 +1,9 @@
+# radiator v.0.0.15 2018-08-17
+
+* `genomic_converter`, `tidy_genomic_data`: bug fix when individuals are integers
+* `fis_summary`: arguments updated
+
+
 # radiator v.0.0.14 2018-08-04
 
 * `filter_dart` and `filter_rad`: can now opt out of HWE filtering. 

R/summary.R

@@ -389,14 +389,9 @@ fis_summary <- function(
   vcf.metadata = TRUE,
   whitelist.markers = NULL,
   monomorphic.out = TRUE,
-  blacklist.genotype = NULL,
   snp.ld = NULL,
   common.markers = TRUE,
   maf.thresholds = NULL,
-  maf.pop.num.threshold = 1,
-  maf.approach = "SNP",
-  maf.operator = "OR",
-  max.marker = NULL,
   blacklist.id = NULL,
   pop.levels = NULL,
   pop.labels = NULL,
@@ -419,21 +414,17 @@ fis_summary <- function(
       data = data,
       vcf.metadata = TRUE,
       blacklist.id = blacklist.id,
-      blacklist.genotype = blacklist.genotype,
       whitelist.markers = whitelist.markers,
       monomorphic.out = monomorphic.out,
-      max.marker = max.marker,
       snp.ld = snp.ld,
       common.markers = common.markers,
       maf.thresholds = maf.thresholds,
-      maf.pop.num.threshold = maf.pop.num.threshold,
-      maf.approach = maf.approach,
-      maf.operator = maf.operator,
       strata = strata,
       pop.levels = pop.levels,
       pop.labels = pop.labels,
       pop.select = pop.select,
-      filename = NULL
+      filename = NULL,
+      verbose = FALSE
     )
   )
 

R/tidy_genomic_data.R

@@ -456,11 +456,15 @@ tidy_genomic_data <- function(
   # Import blacklist id --------------------------------------------------------
   if (!is.null(blacklist.id)) {# With blacklist of ID
     if (is.vector(blacklist.id)) {
-      suppressMessages(blacklist.id <- readr::read_tsv(blacklist.id, col_names = TRUE))
+      suppressMessages(blacklist.id <- readr::read_tsv(
+        blacklist.id,
+        col_names = TRUE,
+        col_types = readr::cols(.default = readr::col_character())))
     } else {
       if (!tibble::has_name(blacklist.id, "INDIVIDUALS")) {
         stop("Blacklist of individuals should have 1 column named: INDIVIDUALS")
       }
+      blacklist.id <- dplyr::mutate_all(.tbl = blacklist.id, .funs = as.character)
     }
     # not for plink file, where it's done after.
     # see plink section to understand

R/tidy_vcf.R

@@ -251,11 +251,15 @@ See this file for the list and count: duplicated.markers.tsv\n\n")
   # Import blacklist id --------------------------------------------------------
   if (!is.null(blacklist.id)) {# With blacklist of ID
     if (is.vector(blacklist.id)) {
-      suppressMessages(blacklist.id <- readr::read_tsv(blacklist.id, col_names = TRUE))
+      suppressMessages(blacklist.id <- readr::read_tsv(
+        blacklist.id,
+        col_names = TRUE,
+        col_types = readr::cols(.default = readr::col_character())))
     } else {
       if (!tibble::has_name(blacklist.id, "INDIVIDUALS")) {
         stop("Blacklist of individuals should have 1 column named: INDIVIDUALS")
       }
+      blacklist.id <- dplyr::mutate_all(.tbl = blacklist.id, .funs = as.character)
     }
     blacklist.id$INDIVIDUALS <- radiator::clean_ind_names(blacklist.id$INDIVIDUALS)
 
@@ -877,6 +881,7 @@ strata_vcf <- function(strata, input, blacklist.id) {
         ))
     } else {
       strata.df <- strata
+      strata.df <- dplyr::mutate_all(.tbl = strata.df, .funs = as.character)
     }
   }
 

R/write_vcf.R

@@ -178,7 +178,7 @@ write_vcf <- function(data, pop.info = FALSE, filename = NULL) {
   readr::write_delim(x = tibble::data_frame(file.date), path = filename, delim = " ", append = TRUE, col_names = FALSE)
 
   # Source ---------------------------------------------------------------------
-  readr::write_delim(x = tibble::data_frame(stringi::stri_join("##source=radiator_v.", utils::packageVersion("radiator"))), path = filename, delim = " ", append = TRUE, col_names = FALSE)
+  readr::write_delim(x = tibble::data_frame(stringi::stri_join("##source=radiator_v.", as.character(utils::packageVersion("radiator")))), path = filename, delim = " ", append = TRUE, col_names = FALSE)
 
   # Info field 1 ---------------------------------------------------------------
   info1 <- as.data.frame('##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">')

README.md

@@ -8,8 +8,8 @@ state and is being actively
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
 [![DOI](https://zenodo.org/badge/14548/thierrygosselin/radiator.svg)](https://zenodo.org/badge/latestdoi/14548/thierrygosselin/radiator)
 
-[![packageversion](https://img.shields.io/badge/Package%20version-0.0.14-orange.svg)](commits/master)
-[![Last-changedate](https://img.shields.io/badge/last%20change-2018--08--04-brightgreen.svg)](/commits/master)
+[![packageversion](https://img.shields.io/badge/Package%20version-0.0.15-orange.svg)](commits/master)
+[![Last-changedate](https://img.shields.io/badge/last%20change-2018--08--17-brightgreen.svg)](/commits/master)
 
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