Added ASW

johnsonra · Apr 19, 2018 · 151191b · 151191b
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diff --git a/ALDdata/DESCRIPTION b/ALDdata/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ALDdata
-Version: 1.2.2
-Date: 2016-01-13
+Version: 1.3.0
+Date: 2018-04-19
 Title: ALDdata
 Author: Randall Johnson <johnsonra@mail.nih.gov>
 Maintainer: Randy Johnson <johnsonra@mail.nih.gov>

diff --git a/ALDdata/data/asw1.RData b/ALDdata/data/asw1.RData
diff --git a/ALDdata/data/asw10.RData b/ALDdata/data/asw10.RData
diff --git a/ALDdata/data/asw11.RData b/ALDdata/data/asw11.RData
diff --git a/ALDdata/data/asw12.RData b/ALDdata/data/asw12.RData
diff --git a/ALDdata/data/asw13.RData b/ALDdata/data/asw13.RData
diff --git a/ALDdata/data/asw14.RData b/ALDdata/data/asw14.RData
diff --git a/ALDdata/data/asw15.RData b/ALDdata/data/asw15.RData
diff --git a/ALDdata/data/asw16.RData b/ALDdata/data/asw16.RData
diff --git a/ALDdata/data/asw17.RData b/ALDdata/data/asw17.RData
diff --git a/ALDdata/data/asw18.RData b/ALDdata/data/asw18.RData
diff --git a/ALDdata/data/asw19.RData b/ALDdata/data/asw19.RData
diff --git a/ALDdata/data/asw2.RData b/ALDdata/data/asw2.RData
diff --git a/ALDdata/data/asw20.RData b/ALDdata/data/asw20.RData
diff --git a/ALDdata/data/asw21.RData b/ALDdata/data/asw21.RData
diff --git a/ALDdata/data/asw22.RData b/ALDdata/data/asw22.RData
diff --git a/ALDdata/data/asw3.RData b/ALDdata/data/asw3.RData
diff --git a/ALDdata/data/asw4.RData b/ALDdata/data/asw4.RData
diff --git a/ALDdata/data/asw5.RData b/ALDdata/data/asw5.RData
diff --git a/ALDdata/data/asw6.RData b/ALDdata/data/asw6.RData
diff --git a/ALDdata/data/asw7.RData b/ALDdata/data/asw7.RData
diff --git a/ALDdata/data/asw8.RData b/ALDdata/data/asw8.RData
diff --git a/ALDdata/data/asw9.RData b/ALDdata/data/asw9.RData
diff --git a/R/helpers.R b/R/helpers.R
@@ -118,3 +118,33 @@ get.LD <- function(chr, pop, keep)
 
     return(LD)
 }
+
+# example of importing data into ALDdata (could be coded better, but this will do)
+if(FALSE)
+{
+    library(ALDdata)
+    library(magrittr)
+    data(hapmap)
+
+    for(i in 1:23)
+    {
+        cat("Processing chromosome", i, '\n')
+
+        phased_raw <- get.phased(i, 'ASW')
+
+        phased <- matrix(nrow = dim(phased_raw)[2] - 2, ncol = dim(phased_raw)[1],
+                         dimnames = list(names(phased_raw)[-(1:2)], phased_raw$rsID))
+
+        tmp <- subset(hapmap, rs %in% phased_raw$rsID)
+        vart <- tmp$var
+        names(vart) <- tmp$rs
+
+        for(j in 1:dim(phased_raw)[1])
+        {
+            phased[,phased_raw$rsID[j]] <- (phased_raw[j,-(1:2)] == vart[phased_raw$rsID[j]]) %>%
+                                           as.numeric()
+        }
+
+        save(phased, file = paste0('../Data/ASW/bin/asw', i, '.RData'))
+    }
+}
diff --git a/README.md b/README.md
@@ -16,6 +16,9 @@ sudo R CMD ISNTALL ALDdata
 Versions
 ========
 
+1.3.0
+  - Added phased data for ASW
+
 1.2.0
   - Added variant allele frequency for all SNPs in YRI, CEU, CHB and JPT
   - Added ALDdata to github