Added test of filtering individuals in LD estimation

comorment · Feb 21, 2024 · b2f536f · b2f536f
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commit b2f536f
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diff --git a/tests/test_LDpred2/run.sh b/tests/test_LDpred2/run.sh
@@ -54,6 +54,9 @@ export fileOutputSNPR=$DIR_DATA/public-data3.rds
 export fileKeepSNPS=/REF/hapmap3/w_hm3.justrs
 export fileOut=$DIR_TESTS/output/public-data.score
 
+# File with subset of individual IDs from the tutorial data
+export fileExtractIndividuals=$DIR_DATA/individual-ids.txt
+
 # BGEN files
 export fileBGEN=$DIR_DATA/example.bgen
 export fileBGENasRDS=$DIR_DATA/example.rds

diff --git a/tests/test_LDpred2/scripts/ld.sh b/tests/test_LDpred2/scripts/ld.sh
@@ -29,6 +29,8 @@ testSuccess $LDE --sumstats $fileSumstats25k rsid --thres-r2 0.2 --chr2use 21 22
 echo "Test restricting on SNPs provide by a SNP list file: $fileKeepSNPS"
 testSuccess $LDE --extract $fileKeepSNPS --file-ld-chr $dirOut/[email protected] --file-ld-map $dirOut/map.rds
 
+echo "Test extracting individuals using $fileExtractIndividuals"
+testSuccess $LDE --extract-individuals $fileExtractIndividuals --file-ld-chr $dirOut/[email protected] --file-ld-map $dirOut/map.rds
 echo "Test sampling individuals (N=400)"
 testSuccess $LDE --sample-individuals 400 --extract $fileKeepSNPS --file-ld-chr $dirOut/[email protected] --file-ld-map $dirOut/map.rds
 # Test this LDpred on this LD (restrict to chromosomes 20-22