Introduction

This script implements XP-BLUP, which improves complex traits prediction in minority populations by combining trans-ethnic and ethnic-specific information. It requires plink (https://www.cog-genomics.org/plink2 v1.90 or later) and gcta (http://cnsgenomics.com/software/gcta/, v1.25.3 or later). Please contact huatang@stanford.edu or hyfang@stanford.edu for questions or bug report.

Usage

./xpblup.sh [--help] [--plink=/usr/local/bin/plink] [--gcta=/usr/local/bin/gcta64] 
[--pheno=./phenos/traindataN4k.pheno] --train=./example_data/trainN4k --test=./example_data/testN2k
 --snplist=./example_data/metaExtract.txt [--outdir=./output] [--outprefix=out]

The parameters in [ ] are optinal if the corresponding command is in system path. Or

./xpblup.sh --train=./example_data/trainN4k --test=./example_data/testN2k --snplist=./example_data/metaExtract.txt

Options

-h, --help Print short help message and exit (Optional)

--plink=plink_loc PLINK location (Optional if plink is in system paths.)

--gcta=gcta_loc GCTA location (Optional if gcta/gcta64 is in system paths.)

--pheno=filename Phenotype file for train data (Optional if phenotype file is included in train_location.fam)

--train=filename Train data for model learning (Required in PLINK binary format: train_location.bed/bim/fam)

--test=filename Test data for model prediction (Required in PLINK binary format: test_location.bed/bim/fam)

--snplist=filename SNP list file that defines SNP set C1 (Required)

--outdir=out_dir Output directory (Default: ./output if not given)

--outprefix=out Output prefix (Default: out if not given)

Example

An example data is included in the data directory:

--metaExtract.txt File defines C1 SNP set

--train4k.bed: binary format of genotype data of the training individuals

--test2k.bed: binary format of genotype data of the test individuals

In this case, the phenotype is in the binary data. Otherwise it can be supplied by --pheno