mxr_summarise: Summarize the GWAS results into an Excel file.

Description Usage Arguments Details Value

Description

mxr_summarise creates an Excel workbook with worksheets for the SNPs and linked SNPs, SNPs and associated genes, annotation of SNPs, annotation of genes, and the identified tag SNPs. A worksheet is also prepared that contains the parameters used in the GWAS run.

Usage

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mxr_summarise(trait = "", gwas_result = "", genotype_bim = "",
  clump_file = "", clump_ranges_file = "", clumped_genes = "",
  clumped_snps = "", reference_annotation = "", output_prefix = "",
  variant_function = "", exonic_variant_function = "", verbose = FALSE)

Arguments

trait

The directory containing the trait phenotype. All GWAS results are also stored into this directory that includes the outputs of this function.

gwas_result

The output of emmax2. (*.ps)

genotype_bim

The .bim file of the genotype data.

clump_file

The .clumped file.

clump_ranges_file

The .clumped.ranges file.

clumped_genes

The .clumped.genes file outputted by the plink file.

clumped_snps

The .clumped.snps file.

reference_annotation

The excel file containing the annotation file that will be used to annotate the genes.

output_prefix

Path and prefix of the output files.

variant_function

Output of annovar.

exonic_variant_function

Output of annovar.

verbose

(Optional) Show verbose output. (DEFAULT=FALSE)

Details

mxr_summarise requires the results of mxr::clump.

Value

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


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