数据格式转换 (整理中)

通过数据格式转换，转换为标准的 TwoSampleMR、SMR、METAL 或 MTAG 格式数据文件，或由这四种格式再转换获得的.sumstats.gz格式数据或其他格式数据。

通用 GWAS 数据清洗与格式转换

这部分适用于所有 GWAS 数据格式转换，类似于 TwoSampleMR 中的format_data()函数。

# format.data.v01.R
sum.dat = format_dat(
  MTAG_dat = TRUE,
  dat = "E:/QTLMR/GWAS/GCST90203354.h.tsv.gz",
  snp_col = "rsid",
  chr_col = "chromosome",
  pos_col = "base_pair_location",
  effect_allele_col = "effect_allele",
  other_allele_col = "other_allele",
  beta_col = "beta",
  se_col = "standard_error",
  eaf_col = "effect_allele_frequency",
  pval_col = "p_value",
  GWAS_name = 'GCST90203354',
  save_path = 'E:/QTLMR/GWAS/MTAG/'
)

FinnGen 数据格式转换

芬兰 R7-R12 汇总信息数据：data/finngen_dat.xlsx

head（finngen_dat)
#     phenocode                                                                name                                    category num_cases num_controls                                                                                     path_https Version                  filename
#        <char>                                                              <char>                                      <char>     <num>        <num>                                                                                         <char>  <char>                    <char>
# 1: HEIGHT_IRN                                     Height, inverse-rank normalized                      Quantitative endpoints    292707            0 https://storage.googleapis.com/finngen-public-data-r10/summary_stats/finngen_R10_HEIGHT_IRN.gz     R10 finngen_R10_HEIGHT_IRN.gz
# 2: WEIGHT_IRN                                     Weight, inverse-rank normalized                      Quantitative endpoints    297440            0 https://storage.googleapis.com/finngen-public-data-r10/summary_stats/finngen_R10_WEIGHT_IRN.gz     R10 finngen_R10_WEIGHT_IRN.gz
# 3:    BMI_IRN                            Body-mass index, inverse-rank normalized                      Quantitative endpoints    290820            0    https://storage.googleapis.com/finngen-public-data-r10/summary_stats/finngen_R10_BMI_IRN.gz     R10    finngen_R10_BMI_IRN.gz
# 4: I9_HYPTENS                                                        Hypertension IX Diseases of the circulatory system (I9_)    122996       289117 https://storage.googleapis.com/finngen-public-data-r10/summary_stats/finngen_R10_I9_HYPTENS.gz     R10 finngen_R10_I9_HYPTENS.gz
# 5:        T2D                               Type 2 diabetes, definitions combined                          Diabetes endpoints     65085       335112        https://storage.googleapis.com/finngen-public-data-r10/summary_stats/finngen_R10_T2D.gz     R10        finngen_R10_T2D.gz
# 6: RX_ANTIHYP Antihypertensive medication - note that there are other indications                     Drug purchase endpoints    222561       189620 https://storage.googleapis.com/finngen-public-data-r10/summary_stats/finngen_R10_RX_ANTIHYP.gz     R10 finngen_R10_RX_ANTIHYP.gz

可以先查询finngen_dat获取对应表型数据，然后使用浏览器下载数据，再进行数据转换。

注意，该数据是基于人类基因组版本：GRCh38 。