mxr_clump: Post-GWAS Processing of Significant Association Peaks.
In roslen/mxr: A Package of GWAS Pipeline Building Blocks

Description Usage Arguments Details Value

mxr_clump determines the clumps of SNPs based on LD along the region that registers a significant association signal with the phenotype. This uses the --clump command of plink. https://www.cog-genomics.org/plink2

mxr_clump(emmax2_results, genotype_prefix, snp_field = "snp_id",
  clump_field = "p", clump_p1 = 1e-05, clump_p2 = 0.01, clump_kb = 200,
  clump_r2 = 0.8, clump_range_border_kb = 20, gene_list = "",
  out_prefix = "", verbose = FALSE)

`emmax2_results`	The fullpath and filename of the results of mxr_associate.
`genotype_prefix`	The fullpath and prefix of the bim/bed/fam plink files.
`snp_field`	The column header for the SNP column in the results file from mxr_associate. (Default: "snp_id")
`clump_field`	The column header for the p-value column in the results file from mxr_associate. (Default: "p")
`clump_p1`	The maximum p-value of the index variants that define each clump. Index variants need to have values between 0 and this p-value. (Default: 0.00001)
`clump_p2`	The maximum association p-value of SNPs that belonging to the clump formed by an index variant. (Default: 0.01)
`clump_kb`	The maximum distance of a clumped SNP from its index variant. (Default: 200)
`clump_r2`	The r-squared value of the clumped SNP with its index variant. (Default: 0.50)
`clump_range_border_kb`	The number of kilobases past the region clump-range region. (Default: 20)
`gene_list`	The list of genes must have the following columns: chromosome, start (bp), end (bp), locus_id. These fields must be tab separated and have an appropriately named column header. The chromosome must be coded to correspond to the plink data. @param out_prefix Path and prefix of the output files.
`verbose`	(Optional) Show verbose output. (DEFAULT=FALSE)

Before running this function, make sure that the mxr_associate function has already been called and that the results are successfully obtained without warnings (that imply fatal errors) or errors.

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

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