harmonize_by_pos: The harmonization of SNP identifiers and alleles.

Description Usage Arguments Author(s)

Description

Function harmonizes SNP identifiers and alleles in the input file according to the provided VCF reference.

Usage

1
harmonize_by_pos(input, output, vcf, id = "markername", chromosome = "chr", position="position", alleles = c("first_allele", "second_allele"), flip = TRUE, sep = "\t", drop = FALSE, gzip = TRUE)

Arguments

input

Name of an input file.

output

Name of an output file.

vcf

Name of the VCF reference.

id

Name of the column containing SNP identifiers in the specified input file.

chromosome

Name of the column containing chromosome names in the specified input file.

position

Name of the column containing chromosomal positions in the specified input file.

alleles

Vector with column names containing first and second alleles in the specified input file.

flip

If TRUE, automatically flips alleles in order to match variant strand in VCF reference. Otherwise, the variant is considered as unresolved.

sep

The field separator character in the specified input file.

drop

If TRUE, then all unresolved variants are dropped from the output file.

gzip

TRUE if output file is in gzip format.

Author(s)

Daniel Taliun, Christian Fuchsberger, Cristian Pattaro


GWAtoolbox documentation built on May 2, 2019, 4:54 p.m.