qtl (version 1.38-4)

mqmprocesspermutation: Convert mqmmulti objects into a scanoneperm object

Description

Function to convert mqmmulti objects into a scanoneperm object, this allows the use of R/qtl methods for permutation analysis that do not support the output of a multiple QTL scan using mqm's outputstructure.

Usage

mqmprocesspermutation(mqmpermutationresult = NULL)

Arguments

mqmpermutationresult

mqmmulti object obtained after performing permutations on a single trait.using the function mqmpermutation

Value

• Output of the algorithm is a scanoneperm object. See also: summary.scanoneperm

See Also

% \input{"inst/docs/Sources/MQM/mqm/standard_seealso.txt"}
• The MQM tutorial:http://www.rqtl.org/tutorials/MQM-tour.pdf
• MQM- MQM description and references
• mqmscan- Main MQM single trait analysis
• mqmscanall- Parallellized traits analysis
• mqmaugment- Augmentation routine for estimating missing data
• mqmautocofactors- Set cofactors using marker density
• mqmsetcofactors- Set cofactors at fixed locations
• mqmpermutation- Estimate significance levels
• scanone- Single QTL scanning % -----^^ inst/docs/Sources/MQM/mqm/standard_seealso.txt ^^-----

Examples

# QTL at chromosome 3
f2qtl <- c(3,15,1,0)

# Mouse genetic map
data(map10)

map10 <- map10[1:3]
# Simulate a F2 Cross
f2cross <- sim.cross(map10,f2qtl,n=100,type="f2")
# Bootstrap MQM mapping on the f2cross
f2result <- mqmpermutation(f2cross,scanfunction=mqmscan)f2result <- mqmpermutation(f2cross,scanfunction=mqmscan, n.perm=2, batchsize=2)

# Create a permutation object
f2perm <- mqmprocesspermutation(f2result)

# What LOD score is considered significant?
summary(f2perm)