Use a SNP relate format before calling snpgdsIBDMLE

tools/Relatedness_gds/Relatedness_gds.script.R

@@ -26,7 +26,15 @@ switch(methode,
         #See https://github.com/zhengxwen/SeqArray/issues/73
         # a temporary solution is to provide a list of snp (here all snps) to the function 
         variant.id <- seqGetData(gds, "variant.id")
+        #sinon il faut transformer le seqarray en format SNPrelate
+        tmp       = tempfile(pattern = "tmp", fileext = "snpRelate")
+     
+        seqGDS2SNP(genofile, tmp, dosage=FALSE, compress.geno="LZMA_RA", compress.annotation="LZMA_RA", optimize=TRUE, verbose=TRUE)
+        #ouvrir le fichier
+        genofile <- snpgdsOpen(tmp)
         pibd <- snpgdsIBDMLE(gds, method = "EM",snp.id=variant.id, autosome.only=FALSE,num.thread=threads)
+     
+        unlink(tmp)
     
     },
     downhill.simplex = {
@@ -34,7 +42,17 @@ switch(methode,
         #See https://github.com/zhengxwen/SeqArray/issues/73
         # a temporary solution is to provide a list of snp (here all snps) to the function 
         variant.id <- seqGetData(gds, "variant.id")
-        pibd <- snpgdsIBDMLE(gds, method = "downhill.simplex",snp.id=variant.id, autosome.only=FALSE,num.thread=threads )
+
+        #sinon il faut transformer le seqarray en format SNPrelate
+        tmp       = tempfile(pattern = "tmp", fileext = "snpRelate")
+     
+        seqGDS2SNP(genofile, tmp, dosage=FALSE, compress.geno="LZMA_RA", compress.annotation="LZMA_RA", optimize=TRUE, verbose=TRUE)
+        #ouvrir le fichier
+        genofile <- snpgdsOpen(tmp)
+        pibd <- snpgdsIBDMLE(genofile, method = "downhill.simplex",snp.id=variant.id, autosome.only=FALSE,num.thread=threads )
+     
+        unlink(tmp)
+
     }
 )