newLG: Re-order markers and re-form linkage groups

In jtlovell/qtlTools: Data Processing and Plotting in Association with R/qtl

Description

newLG Using a named list of markers (list element names = LG names), re-assign markers to linkage groups and re-orient markers. Most of the code is taken from qtl::formLinkageGroups.#' Note: all intermediate calculations are dropped. All chromosomes are set as autosomes.

Usage

newLG(cross, markerList, keep.rf = FALSE)

Arguments

cross	The QTL cross object.
markerList	A named list where element names are the chromosome IDs. Each element must contain a character vector specifying marker names. Markers in cross, but not in markerList will be dropped. Any markers in markerList that are not in markernames(cross) will be dropped.

Details

If any chromosomes are sex-specific, re-class such chromosomes after running newLG: using class(cross$geno[["Xchrom"]]) <- "S" or whatever. The new map has arbitrary cM positions where each marker is separated by 10cM. Run est.map to get true cM positions.

Value

A cross object with markers reordered.

Examples

library(qtlTools)
data(fake.bc)
cross<-fake.bc
## Not run: 
fake.f2<-est.rf(fake.f2)
cross<-fake.f2
#Perturb the marker order and chromosome names
markerlist<-lapply(chrnames(cross), function(x) markernames(cross, chr =x))
names(markerlist) = sample(chrnames(cross),replace = F)
markerList<-lapply(markerlist, function(x) sample(x, replace = F))
#Make new cross with new marker order and chromosome names
cross2<-newLG(cross, markerList = markerList)

# completely perturb the genotype matrix, then pull back together
markerlist = list("1" = sample(markernames(cross), replace = F))
cross.noOrder<-newLG(cross, markerList = markerlist)
lgmar <- formLinkageGroups(cross.noOrder)
print(tab<-table(lgmar))
marlist<-lapply(1:length(unique(lgmar$LG)),
  function(x) rownames(lgmar)[lgmar$LG==x])
cross2<-newLG(cross = cross.noOrder,
              markerList = marlist)

## End(Not run)

jtlovell/qtlTools documentation built on May 20, 2019, 3:14 a.m.