load_g2m_df: Read in the random and the strong datasets

In Alice-MacQueen/CDBNgenomics: Genomics Using the Cooperative Dry Bean Nursery Dataset

Description

Read in the random and the strong datasets

Usage

load_g2m_df(path, numSNPs, suffix)

Arguments

path	File path to the rds files saved from bigsnpr, a character string. Defaults to the working directory.
numSNPs	The number of most significant SNPs selected from each GWAS. Ideally this will give 1 million or fewer total cells in the resultant mash dataframes. Defaults to 1000.
suffix	Character. Optional. Should be the unique suffix used to save cdbn_bigsnp2mashr output as RDS files, if it was used.

Value

A list containing five data frames: the SNPs selected, the B_hat and S_hat matrices for the strong SNP set and for a random SNP set that is twice the size.

Note

Make sure you've removed doubles and NA's from your dataset - or set Shat NA's to a very large number so that that condition will be discounted by mashr.

Alice-MacQueen/CDBNgenomics documentation built on Aug. 18, 2020, 4:39 p.m.