gwas catalog数据库tsv.gz文件,转换成mr smr标准文件

将gwas catalog数据库下载的tsv.gz文件 转换成mr分析.txt文件 转换成smr分析.ma文件

Usage,

prepare_gwascatalog(
  file_path,
  out_path = "./",
  generate_mr = T,
  generate_smr = T,
  col_SNP = "",
  col_effect_allele = "",
  col_other_allele = "",
  col_eaf = "",
  col_beta = "",
  col_se = "",
  col_pval = "",
  col_samplesize = "",
  col_chr = "",
  col_pos = "",
  col_Phenotype = NULL,
  sample_size = NULL
)

参数

file_path

需要转换成mr或smr标准格式的gwas catalog来源的tsv.gz文件

out_path

输出文件的路径，默认为当前工作目录

generate_mr

是否同时输出用于mr分析的标准文件.txt，默认值为T

generate_smr

是否同时输出用于smr分析的标准文件.ma，默认值为T

col_SNP

snp列名映射

col_effect_allele

effect_allele 列名映射

col_other_allele

other_allele 列名映射

col_eaf

eaf 列名映射

col_beta

beta 列名映射

col_se

se 列名映射

col_pval

pval 列名映射

col_samplesize

samplesize 列名映射

col_chr

chr 列名映射

col_pos

pos 列名映射

col_Phenotype

Phenotype列名映射，默认NULL，不取值

sample_size

样本量，默认读取文件样本量，如填写，使用该样本量

值

输出mr标准格式的.txt文件默认当前工作文件夹；输出smr标准格式的.ma文件默认当前工作文件夹

Examples

# 单个文件
prepare_gwascatalog(
  file_path = "28604730-GCST004744-EFO_0000571-Build37.f.tsv.gz",
  out_path="./",
  col_SNP = "variant_id",
  col_effect_allele = "effect_allele",
  col_other_allele = "other_allele",
  col_eaf = "effect_allele_frequency",
  col_beta = "beta",
  col_se = "standard_error",
  col_pval = "p_value",
  col_samplesize = "",
  col_chr = "chromosome",
  col_pos = "base_pair_location"
)
# 多个文件(需要保证列名一致)