mxr_create_annovar_inputs: Create Input File for Annovar.
In roslen/mxr: A Package of GWAS Pipeline Building Blocks

Description Usage Arguments Details Value

mxr_create_annovar_inputs generates the input files needed by annovar.

1 2	mxr_create_annovar_inputs(target_list = "", alleles_from_reference = "", out_prefix = "", verbose = FALSE)

`target_list`	The "target_list" file created by a call to mxr_create_region_file().
`alleles_from_reference`	The "alleles_from_reference" file created by a call to mxr_create_region_file().
`out_prefix`	The output prefix.
`verbose`	(Optional) Show verbose output. (DEFAULT=FALSE)

This function needs to be run before annotating the significant SNPs. It creates three files: 1. the target_list defined from the alleles_from_reference and the, 2. the avinput, and 3. avinput.corrected_chroms files.

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

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