load_mash_df: Read in the random and the strong datasets
In Alice-MacQueen/switchgrassGWAS: Genome Wide Association on Panicum virgatum
Description
Usage
Arguments
Value
Note
View source: R/pvdiv_mash_wrapper.R
Description
Read in the random and the strong datasets
Usage
1
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.
Alice-MacQueen/switchgrassGWAS documentation built on Jan. 23, 2022, 7:55 p.m.
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Description Usage Arguments Value Note
View source: R/pvdiv_mash_wrapper.R
Description
Read in the random and the strong datasets
Usage
1 | 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 |
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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