mxr_annotate: Annotate the significant SNPs.

In roslen/mxr: A Package of GWAS Pipeline Building Blocks

Description

mxr_annotate annotates the significant SNPs using annovar.

Usage

mxr_annotate(avinput = "",
  annovar_reference_db = "~/bin/annovar/rice_msu7/",
  database_build_number = "msu7b",
  aa_matrix_file = "~/bin/annovar/rice_msu7/grantham.matrix",
  out_prefix = "", verbose = FALSE)

Arguments

avinput	Make sure that the chromosome designations match those in the reference genome annotation. (e.g. use the *.corrected_chroms file).
annovar_reference_db	The complete path (with trailing "/") to the annovar local database containing the reference genome.
database_build_number	The database build number of the annovar db.
aa_matrix_file	The grantham.matrix file or any other amino acid substitution "relevance" file.
out_prefix	The output prefix.
verbose	(Optional) Show verbose output. (DEFAULT=FALSE)

Details

Before running this function, mxr_create_annovar_inputs needs to be run first to generate the necessary input files. Note that it is important that the chromosome designation matches exactly the way the chromosome number is designated in the annotation file for the reference genome. For example, "chr01" is not the same as "Chr1", or "Chr01", moreso "1".

Value

TRUE if the PLINK run completed successfully. FALSE, otherwise.

roslen/mxr documentation built on May 27, 2019, 11:32 p.m.