mxr_summarise: Summarize the GWAS results into an Excel file.
In roslen/mxr: A Package of GWAS Pipeline Building Blocks

Description Usage Arguments Details Value

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.

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)

`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)