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Commit c00472b9 authored by Helene Rimbert's avatar Helene Rimbert
Browse files

Correction BUG: Imputation MNI or EMI or NULL

parent 9a4ba08e
......@@ -4,7 +4,6 @@
#gstools_pipeline - derived from bwgs
#@ 2017 Sophie Bouchet, Louis Gautier Tran, CHARMET Gilles
#Version 1.0.0 - Release date: 31/02/2017
#bwgs_gilles_v55.R
#sophie.bouchet@inra.fr
#gilles.charmet@inra.fr
#/////////////////////////////////////////////////////////////////////
......@@ -176,7 +175,7 @@ message("")
#//////////////////////////////////////////////////////////////
#Step 1: Imputation "MNI" or "EMI"
#Step 1: Imputation "MNI" or "EMI" or "NULL"
#//////////////////////////////////////////////////////////////
if((geno.impute.method=="NULL")|(geno.impute.method=="MNI")|(geno.impute.method=="EMI"))
......@@ -220,6 +219,24 @@ message("")
message("Imputed by MNI, EMI...finished.")
if (FIXED!="NULL") {FIXED=round(MNI(FIXED))}
if(geno.impute.method=="NULL")
{
# emi.time.start = system.time()
# geno_impute <- EMI(geno_shrink)
# emi.time.stop = system.time()
geno_impute <- geno
message("NO Imputation.")
message("A part 5x20 of Imputed genotypic matrix:")
print(geno_impute[1:5,1:20],quote=FALSE)
message("")
}
}
......@@ -710,7 +727,7 @@ MAP="NULL",geno.impute.method="NULL",predict.method="GBLUP")
if((geno.impute.method=="NULL")|(geno.impute.method=="MNI")|(geno.impute.method=="EMI"))
{
geno_impute = geno
if(geno.impute.method=="MNI"){
......@@ -774,7 +791,7 @@ MAP="NULL",geno.impute.method="NULL",predict.method="GBLUP")
{
if(geno.reduct.method=="NULL"){
geno_shrink <- geno
geno_shrink <- geno_impute
message("No reduction for genomic data.")
new.geno.size <- dim(geno_shrink)
}
......
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