format_data: Format GWAS summary data.

In YangLabHKUST/MR-APSS: The MRAPSS package implement the MR-APPSS approach to test for the causal effect of an exposure on a outcome disease.

Format GWAS summary data.

Description

Reads in GWAS summary data. Infer Zscores from p-values and signed satatistics. This function is adapted from the format_data() function in MRCIEU/TwoSampleMR.

Usage

format_data(
  dat,
  snps.merge = w_hm3.snplist,
  snps.remove = MHC.SNPs,
  snp_col = "SNP",
  b_col = "b",
  or_col = "or",
  se_col = "se",
  freq_col = "freq",
  A1_col = "A1",
  A2_col = "A2",
  p_col = "p",
  ncase_col = "ncase",
  ncontrol_col = "ncontrol",
  n_col = "n",
  n = NULL,
  z_col = "z",
  info_col = "INFO",
  log_pval = FALSE,
  chi2_max = NULL,
  min_freq = 0.05
)

Arguments

dat	Data frame. Must have header with at least SNP A1 A2 signed statistics pvalue and sample size.
snps.merge	Data frame with SNPs to extract. must have headers: SNP A1 and A2. For example, the hapmap3 SNPlist.
snps.remove	a set of SNPs needed to be removed. For example, the SNPs in MHC region.
snp_col	column with SNP rs IDs. The default is SNP.
b_col	Name of column with effect sizes. The default is b.
se_col	Name of column with standard errors. The default is se.
freq_col	Name of column with effect allele frequency. The default is frew.
A1_col	Name of column with effect allele. Must contain only the characters "A", "C", "T" or "G". The default is A1.
A2_col	Name of column with non effect allele. Must contain only the characters "A", "C", "T" or "G". The default is A2.
p_col	Name of column with p-value. The default is p.
ncase_col	Name of column with number of cases. The default is ncase.
ncontrol_col	Name of column with number of controls. The default is ncontrol.
n_col	Name of column with sample size. The default is n.
n	Sample size
z_col	Name of column with Zscore. The default is z.
info_col	Name of column with inputation Info. The default is info.
log_pval	The pval is -log10(p_col). The default is FALSE.
chi2_max	SNPs with tested chi^2 statistics large than chi2_max will be removed.The default is 80
min_freq	SNPs with allele frequecy less than min_freq will be removed.The default is 0.05
or_col:	Name of column with odds ratio. The default is or.
n_qc	Whether to remove SNPs according to the sample size of SNPs. The default is FALSE.

Value

data frame wih headers: SNP: rsid; A1: effect allele; A2: non effect allel; Z: Z score; N: sample size; chi2: chi square statistics; P: p-value.

YangLabHKUST/MR-APSS documentation built on April 13, 2025, 7:56 p.m.