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Get chromosome (phys.chr) and physical position in cM (phys.pos), along with the LOD score (peak.lod) at the peak position (peak.pos), and the chromosome where the peak is located (peak.chr). Some candidates may map to the same chromosome where they are physically located.
GetCandReg(highobj, annot, traits)
GetCisCandReg(highobj, cand.reg, lod.thr = NULL)
GetCoMappingTraits(highobj, cand.reg)data frame with annotation information; must have first column as unique identifier, third column as chromosome, and fifth column as position in cM; typically column 2 has gene name, and column 4 has position in Mb
names of traits to examine as candidate regulators; names must
correspond to phenotypes in cross object
data frame with candidate regulator; see value section below
LOD threshold; restrict to intervals above this value if
not NULL
GetCoMappingTraits returns a list with each element being the
names of co-mapping traits for a particular name in traits.
GetCandReg returns a data frame while GetCisCandReg
returns a list with a similar candidate regulator data frame as the
element cis.reg, and the index of trait names as the element
cis.index. The elements of the candidate regulator data frame
are as follows (peak.pos.lower and peak.pos.upper only
for GetCisCandReg):
name of trait, which might be a gene name
chromosome on which gene physically resides
physical position (in cM)
chromosome where peak LOD is located
position of peak (in cM)
LOD value at peak
lower and upper bounds
of the 1.5-LOD support interval around peak.pos
Traits that map to positions close to their physical locations are said
to map in cis (local linkages).
Traits that map to positions away from their physical locations are said to map in
trans (distal linkages). There is no unambiguous way to determine how close a trait needs to
map to its physical location in order to be classified as cis. Our choice is to classify a trait as
cis if the 1.5-LOD support interval (Manichaikul et al. 2006) around the LOD peak contains
the trait's physical location, and if the LOD score at its physical location is higher the the LOD
threshold. The function GetCisCandReg determines which of the candidate regulators map in
cis. The function GetCoMappingTraits returns a list with the putative
targets of each trait. A trait is included in the putative target list of
a trait when its LOD peak is greater than lod.thr and the
drop LOD support interval around the peak contains the location
of the trait's QTL.
The function JoinTestOutputs currently relies on external files
that contain results of FitAllTests. It needs to be
rewritten to save space.
Manichaikul et al. (2006) Genetics
# NOT RUN {
## data(CMSTCross) is loaded lazily.
CMSTscan <- scanone(CMSTCross, pheno.col = 1:3, method = "hk")
CMSThigh <- highlod(CMSTscan)
traits <- names(CMSTCross$pheno)
annot <- data.frame(name = traits, traits = traits, chr = rep(1, 3),
Mb.pos = c(55,10,100))
annot$cM.pos <- annot$Mb.pos
cand.reg <- GetCandReg(CMSThigh, annot, traits)
cis.cand.reg <- GetCisCandReg(CMSThigh, cand.reg)
comap.targets <- GetCoMappingTraits(CMSThigh, cand.reg)
# }
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