snpgdsBED2GDS() allows a single file name

without the extended file names (.bed, .fam, .bim)
zhengxwen · Jan 1, 2019 · 3b70897 · 3b70897
1 parent 277cdb8
commit 3b70897
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Showing 4 changed files with 16 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: SNPRelate
 Type: Package
 Title: Parallel Computing Toolset for Relatedness and Principal Component
         Analysis of SNP Data
-Version: 1.17.1
-Date: 2018-12-20
+Version: 1.17.2
+Date: 2019-01-01
 Depends: R (>= 2.15), gdsfmt (>= 1.8.3)
 LinkingTo: gdsfmt
 Imports: methods

diff --git a/NEWS b/NEWS
@@ -1,7 +1,8 @@
-CHANGES IN VERSION 1.17.1
+CHANGES IN VERSION 1.17.1-1.17.2
 -------------------------
 
-    o 
+    o `snpgdsBED2GDS()` allows a single file name without the extended file
+      names (.bed, .fam, .bim)
 
 
 CHANGES IN VERSION 1.16.0

diff --git a/R/Conversion.R b/R/Conversion.R
@@ -438,6 +438,13 @@ snpgdsBED2GDS <- function(bed.fn, fam.fn, bim.fn, out.gdsfn, family=FALSE,
 {
     # check
     stopifnot(is.character(bed.fn), length(bed.fn)==1L)
+    if (missing(fam.fn) && missing(bim.fn))
+    {
+        fn <- gsub("\\.bed$", "", bed.fn, ignore.case=TRUE)
+        bed.fn <- paste(fn, ".bed", sep="")
+        fam.fn <- paste(fn, ".fam", sep="")
+        bim.fn <- paste(fn, ".bim", sep="")
+    }
     stopifnot(is.character(fam.fn), length(fam.fn)==1L)
     stopifnot(is.character(bim.fn), length(bim.fn)==1L)
     stopifnot(is.character(out.gdsfn), length(out.gdsfn)==1L)

diff --git a/man/snpgdsBED2GDS.Rd b/man/snpgdsBED2GDS.Rd
@@ -12,9 +12,10 @@ snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, out.gdsfn, family=FALSE,
 }
 \arguments{
     \item{bed.fn}{the file name of binary file, genotype information}
-    \item{fam.fn}{the file name of first six columns of \code{".ped"}}
-    \item{bim.fn}{the file name of extended MAP file:
-        two extra columns = allele names}
+    \item{fam.fn}{the file name of first six columns of \code{".ped"}; if it is
+        missing, }
+    \item{bim.fn}{the file name of extended MAP file: two extra columns =
+        allele names; if it is missing, }
     \item{out.gdsfn}{the output GDS file}
     \item{family}{if \code{TRUE}, to include family information in the
         sample annotation}