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calc_prs_cross_ld.sh
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calc_prs_cross_ld.sh
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#!/bin/bash
source constants_.sh
source parse_args.sh "$@"
source init_args_cross.sh
method="ld"
prs_prefix="prs.cross.${method}${sub}"
ds_prefix="ds${sub}"
#ds_prefix="ds_flipped${sub}"
mkdir -p ${prs_path}ldpred || true
if [[ ${stage} -le 1 ]]; then
Rscript ldpred.R --discovery=${discovery} \
--target_train=${target_train} --imp_train=${imp_train} \
--target_test=${target_test} --imp_test=${imp_test} \
--suffix=${suffix} --rep=${rep} --analysis_type="cross";
fi
if [[ ${stage} -le 2 ]]; then
for cur_hp in {1..102}; do
if [[ -f ${prs_path}ldpred/${prs_prefix}${train_suffix}.${cur_hp}.weights ]]; then
plink --bfile ${imp_test_path}${ds_prefix}${test_suffix} \
--score ${prs_path}ldpred/${prs_prefix}${train_suffix}.${cur_hp}.weights 2 5 6 \
--exclude ${imp_test_path}ds.dupvar \
--out ${prs_path}${prs_prefix}${test_suffix}.${cur_hp} # ${prs_path}ldpred/${prs_prefix}${train_suffix}.${cur_hp}.weights 2 5 6 \ $PRS_PRSS/bcac_onco_eur-5pcs_bcac_onco_aj/impX_new/rep_75/ldpred/prs.cv.ld___1_5_train.1500.weights 1 5 6 \
fi
done
fi
if [[ ${stage} -le 3 ]]; then
Rscript calc_metrics_cross_${method}.R --discovery=${discovery} \
--target_train=${target_train} --imp_train=${imp_train} \
--target_test=${target_test} --imp_test=${imp_test} \
--suffix=${suffix} --rep=${rep} --analysis_type="cross";
fi