Get genetic information on candidate regulators and co-mapping traits.

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Description

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.

Usage

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GetCandReg(highobj, annot, traits)
GetCisCandReg(highobj, cand.reg, lod.thr = NULL)
GetCoMappingTraits(highobj, cand.reg)

Arguments

highobj

data frame from highlod, which is sparse summary of high LODs in large scanone object

annot

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

traits

names of traits to examine as candidate regulators; names must correspond to phenotypes in cross object

cand.reg

data frame with candidate regulator; see value section below

lod.thr

LOD threshold; restrict to intervals above this value if not NULL

Details

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.

Value

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):

gene

name of trait, which might be a gene name

phys.chr

chromosome on which gene physically resides

phys.pos

physical position (in cM)

peak.chr

chromosome where peak LOD is located

peak.pos

position of peak (in cM)

peak.lod

LOD value at peak

peak.pos.lower,peak.pos.upper

lower and upper bounds of the 1.5-LOD support interval around peak.pos

Author(s)

Elias Chaibub Neto

References

Manichaikul et al. (2006) Genetics

See Also

highlod, FitAllTests, scanone

Examples

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## 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)