find_leadsnps: Find the lead SNP for each phenotype in each region.
In kjgleason/primo: Package in R for Integrative Multi-Omics association analysis

Determine the lead SNP for each phenotype in each region based on summary statistics. A data.table will be returned containing lead SNP information for each region.

1 2	find_leadsnps(data, snp_col, pheno_cols, stat_cols, data_type = "pvalue", suffices = NULL)

`data`	data.table. Each row will be a SNP-phenotype combination with statistics necessary to determine the lead SNP in each phenotype region.
`snp_col`	character string of the column name of the SNP.
`pheno_cols`	character vector of the column names of the phenotypes.
`stat_cols`	character vector of the column names of statistics to be used to determine lead SNPs.
`data_type`	character string denoting type of statistics being used. Must be either "pvalue" or "tstat".
`suffices`	character vector denoting suffices to use for the names of the lead SNP columns (optional). If `NULL`, consecutive integers will be assigned.

A data.table containing information about the lead SNPs and associated statistics. The columns will be pheno_cols followed by two columns for each phenotype: the name of the lead SNP and the value of the statistic for that lead SNP in that phenotype.

kjgleason/primo documentation built on Sept. 7, 2021, 5:21 p.m.