a new example file for imputed dosages

seqExampleFileName("dosage")

Author: zhengxwen

NEWS

@@ -1,4 +1,4 @@
-CHANGES IN VERSION 1.49.6
+CHANGES IN VERSION 1.49.7
 -------------------------
 
 NEW FEATURES
@@ -16,6 +16,8 @@ NEW FEATURES
 
     o new 'alt' & 'ns' in `seqGetAF_AC_Missing()`
 
+    o new 'dosage' in `seqExampleFileName()`
+
 UTILITIES
 
     o tweak the display of `seqGDS2BED()`

R/Utilities.R

@@ -38,18 +38,16 @@
 #######################################################################
 # Get the file name of an example
 #
-seqExampleFileName <- function(type=c("gds", "vcf", "KG_Phase1"))
+seqExampleFileName <- function(type=c("gds", "vcf", "KG_Phase1", "dosage"))
 {
     type <- match.arg(type)
-    switch(type,
-        gds =
-            system.file("extdata", "CEU_Exon.gds", package="SeqArray"),
-        vcf =
-            system.file("extdata", "CEU_Exon.vcf.gz", package="SeqArray"),
-        KG_Phase1 =
-            system.file("extdata", "1KG_phase1_release_v3_chr22.gds",
-                package="SeqArray")
+    fn <- switch(type,
+        gds = "CEU_Exon.gds",
+        vcf = "CEU_Exon.vcf.gz",
+        KG_Phase1 = "1KG_phase1_release_v3_chr22.gds",
+        dosage = "Imputed_dosages.gds"
     )
+    system.file("extdata", fn, package="SeqArray")
 }
 
 

inst/extdata/Imputed_dosages.gds

@@ -99,6 +99,14 @@ head(v)
 
 # close the GDS file
 seqClose(f)
+
+# A GDS file with imputed dosages
+ds_fn <- seqExampleFileName("dosage")
+ds_fn
+
+str(seqGetAF_AC_Missing(ds_fn, alt=FALSE))
+str(seqGetAF_AC_Missing(ds_fn, alt=TRUE))
+str(seqGetAF_AC_Missing(ds_fn, minor=TRUE))
 }
 
 \keyword{gds}

man/seqAlleleFreq.Rd

@@ -5,16 +5,17 @@
     The example files of VCF and GDS format.
 }
 \usage{
-seqExampleFileName(type=c("gds", "vcf", "KG_Phase1"))
+seqExampleFileName(type=c("gds", "vcf", "KG_Phase1", "dosage"))
 }
 \arguments{
-    \item{type}{either "gds" (by default) or "vcf"}
+    \item{type}{"gds" (by default), "vcf", "KG_Phase1" or "dosage"}
 }
 \value{
     Return the path of a VCF file in the package if \code{type="vcf"}, or
-the path of a GDS file if \code{type="gds"}. If \code{type="KG_Phase1"},
+the path of a GDS file if \code{type="gds"}; if \code{type="KG_Phase1"},
 return the path of GDS file on Chromosome 22 of the 1000 Genomes Phase 1
-project.
+project; if \code{type="dosage"}, return the path of GDS file with imputed
+allele dosages.
 }
 
 \author{Xiuwen Zheng}
@@ -25,6 +26,8 @@ seqExampleFileName("gds")
 seqExampleFileName("vcf")
 
 seqExampleFileName("KG_Phase1")
+
+seqExampleFileName("dosage")
 }
 
 \keyword{gds}