New in v.0.1.3 : Map-Independent imputations using Random Forest or t…

…he most frequent allele of a VCF file produced by STACKS.
thierrygosselin · Sep 3, 2015 · bf98fcd · bf98fcd
1 parent baa746d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: stackr
 Type: Package
 Title: GBS/RAD Data Exploration, Manipulation and Visualization using R
-Version: 0.1.2
-Date: 2015-07-16
+Version: 0.1.3
+Date: 2015-09-03
 Encoding: UTF-8
 Authors@R: c(
   person("Thierry", "Gosselin", email = "[email protected]", role = c("aut", "cre")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -48,6 +48,7 @@ export(summary_stats_pop)
 export(summary_stats_vcf_tidy)
 export(sumstats_prep)
 export(table_low_coverage_summary)
+export(vcf_imputation)
 export(whitelist_loci)
 export(whitelist_loci_snp)
 export(whitelist_loci_vcf)

diff --git a/R/haplo2colony.R b/R/haplo2colony.R
@@ -743,7 +743,7 @@ haplo2colony <- function(haplotypes.file,
         # Automatically select all the core -1 
         options(rf.cores=detectCores()-1, mc.cores=detectCores()-1)
       } else {
-        options(rf.cores = parallel.core, mc.cores = mc.cores)
+        options(rf.cores = parallel.core, mc.cores = parallel.core)
       }
 
       # imputations using Random Forest with the package randomForestSRC

diff --git a/R/haplo2genepop.R b/R/haplo2genepop.R
@@ -371,7 +371,7 @@ haplo2genepop <- function(haplotypes.file,
         # Automatically select all the core -1 
         options(rf.cores=detectCores()-1, mc.cores=detectCores()-1)
       } else {
-        options(rf.cores = parallel.core, mc.cores = mc.cores)
+        options(rf.cores = parallel.core, mc.cores = parallel.core)
       }
 
       # imputations using Random Forest with the package randomForestSRC

diff --git a/R/haplo2genind.R b/R/haplo2genind.R
@@ -315,7 +315,7 @@ haplo2genind <- function(haplotypes.file,
         # Automatically select all the core -1 
         options(rf.cores=detectCores()-1, mc.cores=detectCores()-1)
       } else {
-        options(rf.cores = parallel.core, mc.cores = mc.cores)
+        options(rf.cores = parallel.core, mc.cores = parallel.core)
       }
 
       # imputations using Random Forest with the package randomForestSRC