GCTA-fastBAT — postgwas_gcta_fastBAT • DrugTargetMR

fastBAT is a fast set-based association analysis for human complex traits using summary-level data from genome-wide association studies (GWAS) and linkage disequilibrium (LD) data from a reference sample with individual-level genotypes. 使用此方法请引用, PMID: 27604177。

Usage,

postgwas_gcta_fastBAT(
  gcta_exe,
  file_path,
  bfile,
  maf = 0.01,
  glist = "y:/data_smr/glist-hg19",
  thread_num = 4,
  out_path = "./",
  out_prefix = "fastBAT"
)

参数

gcta_exe: gcta可执行文件地址
file_path: gwas文件地址，为smr标准格式 .ma 结尾的文件
bfile: LD连锁不平衡bfile文件
maf: maf过滤值，默认0.01
glist: 基因信息文件，需根据输入GWAS文件的参考基因组版本选择
thread_num: 线程数，默认4
out_path: 输出文件地址
out_prefix: 输出文件前缀

Examples

postgwas_gcta_fastBAT(
 gcta_exe = "e:/gcta-1.94.1-Win-x86_64/exe/gcta-win-1.94.1.exe",
 file_path = "./6_data_prepare_ma/AAA_CAD_hg19_avsnp151_腹主动脉瘤meta-AAAgen-final-sumstat.ma",
 bfile = "f:/data_ref/1kg.v3/EUR",
 glist = "y:/data_smr/glist-hg19",
 out_path = "./6_Gene_based_analysis",
 out_prefix = "AAA_CAD_hg19_avsnp151_腹主动脉瘤"
)