prepvar: Preparing variant database.

In BartBroeckx/Mendelian: Variant Analysis for Mendelian Disorders

Description

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

Usage

prepvar(y, MAF, reference)

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.

Details

This function prepares the variants from a 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"). For large files, running time can be quite long. An alternative supporting parallel computing is prepvarpar. For the actual filtering, use varfilter.

Author(s)

Bart Broeckx

Examples

y <- SNP
reference <- "refNCBI"
MAF <- 0.03
a <-prepvar(y, MAF, reference)

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