scanInv: Inversion scan

In inveRsion: Inversions in genotype data

Description

This function scans a whole chromosome in search for inversion events. The scan is done by fitting an inversion model to all segments in the chromosome with fixed length size.

Usage

scanInv(objectHaploCode, window, maxSteps = 30, geno = FALSE, saveRes = TRUE, saveBlocks=TRUE)

Arguments

objectHaploCode	Object of class HaploCode produced by the codeHaplo function.
window	numeric, size of the window in mega-basis.
maxSteps	numeric, maximum number of iteration in the EM algorithm for the inversion model
geno	logical. Whether the original data is genotypes or phases haplotypes.
saveRes	logical. Whether results should be saves into file invRes.RData
saveBlocks	logical. Whether save blocks for each candidate break point.

Details

The function processes the haplotypes coded in objectHaploCode. If subsequent re-runs are requires for different window sizes, this object can be omitted. The function will thus search the local directory for previous results to speed up further scans.

Value

object of class scan

Author(s)

Alejandro Caceres [e-mail]

See Also

HaploCode , scan

Examples

data(hapCode)
window<-0.5
scanRes<-scanInv(hapCode,window=window,saveRes=FALSE,geno=FALSE,saveBlocks=FALSE)
scanRes
plot(scanRes)

inveRsion documentation built on Nov. 8, 2020, 5:08 p.m.