Description Usage Arguments Value Note Examples
View source: R/pvdiv_bigsnp2mashr.R
This function converts bigsnpr output, saved as rds files to the specified path, to four dataframes used in the R package mashr. It can clump SNPs based on LD and the maximum -log10(p-value) across all included GWAS. It can also set the random effect data frames to come from a subsample of SNPs clumped by MAF and LD.
1 2 3 4 5 6 7 8 9 10 11 12 |
path |
File path to the rds files saved from bigsnpr, a character string. Defaults to the working directory. |
snp |
The "bigSNP" object used to run the gwas; needed if clump is TRUE. Load with bigsnpr::snp_attach(). |
gwas_rds |
A character vector of saved gwas rds objects from bigsnpr. If NA, all *.rds files in the path will be used. |
phenotypes |
A character vector of phenotype names for the GWAS RDS objects. Must be the same length as gwas_rds, or NA. If NA, these will be the rds file names. |
clump |
Logical. Should SNPs be clumped by LD & p-value to standardize signal strength across different LD blocks? Default is TRUE. |
scaled |
Logical. Should marker effects in each condition be scaled to fall between -1 and 1? Default is TRUE. |
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. |
model |
Regression used in bigstatsr. One of "logistic" or "linear". Default is "linear". |
saveoutput |
Logical. Should the function's output also be saved to RDS files? Default is FALSE. |
suffix |
Character. Optional. If the function's output is saved to RDS files, what unique suffix should be used? |
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.
To create a vector of phenotype names, use the
pvdiv_results_in_folder
function.
1 2 3 4 5 6 7 8 9 10 11 | ## Not run: bigsnp2mashr(path = system.file("inst/extdata"), numSNPs = 20,
model = "linear")
## End(Not run)
## Not run: bigsnp2mashr(numSNPs = 10000, model = "logistic")
## Not run: bisgnp2mashr(numSNPs = 20000, model = "linear", saveoutput = TRUE)
## Not run: phenotype_vector <- pvdiv_results_in_folder(path = system.file(
"inst/extdata"))
numSNPs <- 1000000 / length(phenotype_vector)^2
bigsnp2mashr(phenotypes = phenotype_vector, numSNPs = numSNPs,
model = "linear", saveoutput = TRUE)
## End(Not run)
|
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