其他数据库来源文件,转换成mr smr标准文件

将其他数据库来源文件， 转换成mr分析.txt文件 转换成smr分析.ma文件

Usage,

prepare_others(
  file_path,
  out_path = "./",
  generate_mr = T,
  generate_smr = T,
  sep = "\t",
  comment = "#",
  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标准格式的文件，可以是.gz文件也可以是文本文件。 如果确定是同一批GWAS数据，源数据的数据格式和形式一致，列名一致，可以输入1个或者多个待处理文件。

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

sep

文件分割符，默认"\t"。

comment

注释符号，默认"#"

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

# 单个文件预处理
prepare_others(file_path = "acyp2_12812_25.txt.gz",
out_path = "./",
generate_smr = F,
col_SNP = "rsid",
col_effect_allele = "Allele1",
col_other_allele = "Allele2",
col_eaf = "Freq1",
col_beta = "Effect",
col_se = "StdErr",
col_pval = "Pvalue",
col_samplesize = "TotalSampleSize",
col_chr = "chr",
col_pos = "pos")

# 多个文件预处理。一定要保证是同一批数据，数据格式和形式一致，列名一致。
prepare_others(file_path = c("acyp2_12812_25.txt.gz","ada11_6586_19.txt.gz","ada15_15455_40.txt.gz"),
out_path = "./",
generate_smr = F,
col_SNP = "rsid",
col_effect_allele = "Allele1",
col_other_allele = "Allele2",
col_eaf = "Freq1",
col_beta = "Effect",
col_se = "StdErr",
col_pval = "Pvalue",
col_samplesize = "TotalSampleSize",
col_chr = "chr",
col_pos = "pos")