Read in the random and the strong datasets

Read in the random and the strong datasets

load_mash_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.