run.sim.scans: Runs the genome scans of the simulated data output by...

In gkeele/sparcc: Simulated Power Analysis in the Realized Collaborative Cross

Description

This function takes the output from sim.CC.data() and performs the genome scans. Internally it runs the require QR decompositions, which it can save for later if specified.

Usage

run.sim.scans(sim.data, scan.index = NULL, chr = "all",
  just.these.loci = NULL, use.progress.bar = FALSE,
  print.scans.progress = FALSE, all.sim.qr = NULL,
  return.all.sim.qr = TRUE, ...)

Arguments

sim.data	Output simulated data from sim.CC.data().
scan.index	DEFAULT: NULL. If NULL, it performs scans for all simulated data sets stored in sim.data. If given a vector of integers, representing the simulation index, it will only run scans for those phenotypes.
chr	DEFAULT: "all". Specifies which chromosomes to scan.
just.these.loci	DEFAULT: NULL. If NULL, all loci in genome cache are scanned.
use.progress.bar	DEFAULT: FALSE. Specifies whether to use a progress bar for qr decompositions and genome scans.
print.scans.progress	DEFAULT: FALSE. Specifies whether to output a message that indicates the number of scans completed.
all.sim.qr	DEFAULT: NULL. If NULL, necessary qr decompositions are performed, which will slow down the function significantly. If non-NULL, it expects either output from extract.qr for a single sample of CC lines, or a list of output for multiple samples.
return.all.sim.qr	DEFAULT: TRUE. Saves the qr decompositions for later use, though will make output substantially larger. Could then be used for later scans with the same set of CC lines.

Examples

run.sim.scans()

gkeele/sparcc documentation built on May 28, 2019, 5:43 a.m.