Merge pull request #80 from green-striped-gecko/dev

Dev

DESCRIPTION

@@ -2,8 +2,8 @@ Package: dartR
 Type: Package
 Title: Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide
     Restriction Fragment Analysis
-Version: 1.3.3
-Date: 2019-06-06
+Version: 1.3.4
+Date: 2019-06-14
 Authors@R: c(
             person("Bernd", "Gruber", email="bernd.gruber@canberra.edu.au", role=c("aut","cre")), 
             person("Arthur", "Georges", email="georges@aerg.edu.au", role="aut"),

NAMESPACE

@@ -20,6 +20,7 @@ export(gl.drop.pop)
 export(gl.edit.recode.ind)
 export(gl.edit.recode.pop)
 export(gl.filter.callrate)
+export(gl.filter.callrate.loc.pop)
 export(gl.filter.cloneid)
 export(gl.filter.hamming)
 export(gl.filter.heterozygosity)

R/gl.filter.callrate.loc.pop.r

@@ -0,0 +1,23 @@
+#' Filter loci in a genlight adegenet object based on call rate and population level. 
+#'
+#' This funciton is a convenience function that filters callrate for the set threshold for each population and then returns a genlight object where each loci of every population passes the threshold of the call rate filter. For more details on call rates see gl.filter.callrate.
+#' @param  x - genlight object to be filtered
+#' @param threshold threshold on call rate for loci for each population (see gl.filter.callrate for details.)
+#' @return The filtered genlight or genind object
+#' @export
+#' @examples
+#' gg <- gl.filter.callrate.loc.pop(testset.gl, 0.9)
+
+gl.filter.callrate.loc.pop <- function(x, threshold){
+
+  pops <- seppop(x) 
+  ll <- lapply(pops, function(x) locNames(gl.filter.callrate(x, method = "loc", threshold = threshold, verbose = 0)))
+  locall <- Reduce(intersect, ll)
+  index <- which(locNames(x) %in% locall)
+  x <- x[ , locall]
+  x@other$loc.metrics <- x@other$loc.metrics[locall,]
+  #add to history
+  nh <- length(x@other$history)
+  x@other$history[[nh + 1]] <- match.call()
+  return(x)
+}