Harmonise list of GWAS data to have same variants, same effect allele, and to remove duplicate snps

Harmonise list of GWAS data to have same variants, same effect allele, and to remove duplicate snps

harmoniseGWAS(
  obsgwas,
  minMAF = 0.005,
  minINFO = 0.4,
  beta_colname = "beta",
  se_colname = "SE",
  snpID_colname = "rsID",
  EA_colname = "EA",
  NEA_colname = "NEA",
  EAfreq_colname = "EAF",
  BP_colname = "BP",
  pvalue_colname = "p_value",
  INFO_colname = "INFO"
)

Arguments

obsgwas

list of GWAS data.frames with column names as specified in the other arguments

minMAF

only variants with MAF > minMAF in all GWAS are retained; default is 0.005

minINFO

only variants with INFO > 0.4 in all GWAS are retained; default is 0.4

beta_colname

text column name for the effect estimates in each obsGWAS data.frame; default "BETA"

se_colname

text column name for the effect estimate standard errors in each obsGWAS data.frame; default "SE"

snpID_colname

text column name for the effect estimates in each obsGWAS data.frame; default "SNP"

EA_colname

text column name for the effect allele in each obsGWAS data.frame; default "EA"

NEA_colname

text column name for the non-effect allele in each obsGWAS data.frame; default "NEA"

EAfreq_colname

text column name for the effect allele frequency (EAF) in each obsGWAS data.frame; default "EAF"

BP_colname

text column name for the base-pair position in each obsGWAS data.frame; default "BP"

pvalue_colname

text column name for the p-value in each obsGWAS data.frame; default "p_value"

INFO_colname

text column name for the INFO score in each obsGWAS data.frame; default "INFO"

Value

outputs the list of input GWAS data such that they contain the same variants, have the same effect allele (flip where needed), and duplicates (by base-pair position) are removed, retaining the variant with highest INFO score

Author

Jenn Asimit