prepvarpar: Preparing variant database (parallel).

Description Usage Arguments Details Examples

View source: R/code.R

Description

prepvarpar is used to prepare a large variant database for further filtering with varfilter.

Usage

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prepvarpar(y, MAF, reference, nproc)

Arguments

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.

Details

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.

Examples

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#library(doParallel)
#registerDoParallel()
# nproc <-getDoParWorkers()
# a <-prepvarpar(SNP, 0.03,"refNCBI", 1)

BartBroeckx/Mendelian documentation built on May 5, 2019, 10:27 a.m.