polylinkr: Compute null distribution and probability estimation of gene...

In ACAD-UofA/PolyLinkR: Polygenic Pathway Enrichment Accounting for Genetic Linkage

Description

This is the core function of PolyLinkR, it runs the permuation algorithm that creates a random mapping of genomic scores while preserving the inherent linkage disequilibrium amongt the different genomic regions. This process performed iteratively to generate a null distribution for testing enrichment in biological pathways or gene sets.

Usage

polylinkr(
  set.info,
  obj.info,
  set.obj,
  n.cores = NA,
  emp.nruns = 10000,
  NN = 1000
)

Arguments

set.info	data.frame: four required fields; gene IDs, associated scores, chromosome, and start position
obj.info	data.frame: two required fields; genomic regions and associated scores
set.obj	data.frame: two required fields; genomic regions and associated scores
n.cores	integer: number of cores to run in parallel
emp.nruns	integer: number of iterations used to compute null
NN	integer: subset of interations for summary statistic calculations; default = 1000

Value

Returns a data.table.

See Also

PolyLinkR_SetInfo, PolyLinkR_SetObj

Examples

output = polylinkr(obj.info = Anatolia_EF_CLR, 
             set.info = PolyLinkR_SetInfo, set.obj = PolyLinkR_SetObj,
             n.cores = 8, emp.nruns = 1000, NN = 10000)

ACAD-UofA/PolyLinkR documentation built on Dec. 31, 2020, 9:44 a.m.