Description Usage Arguments Details Examples
prepvarpar is used to prepare a large variant database for further filtering with varfilter.
1 | prepvarpar(y, MAF, reference, nproc)
|
y |
the data frame containing the variants. |
MAF |
optional numeric, the MAF of the non-reference variants to be retained for filtering. |
reference |
the column containing the reference sequence in the y data frame. |
nproc |
the number of cores or workers used for parallel computing. |
This function prepares the variants from a large database like dbSNP to be used for filtering variants in cases. MAF is optional and specifies a minimum allele frequency for the database variants to be retained for variant filtering. The input of y should be the standard output of the UCSC table browser ("all fields from selected table"). This function allows parallel computing, leading to substantial time improvement when entire databases are used. If parallel computing is not necessary or not possible, use prepvar.Prior to running this function, call function registerDoParallel from the doParallel package to permit parallel computing.
1 2 3 4 | #library(doParallel)
#registerDoParallel()
# nproc <-getDoParWorkers()
# a <-prepvarpar(SNP, 0.03,"refNCBI", 1)
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