GetCandReg {qtlhot} | R Documentation |
Get genetic information on candidate regulators and co-mapping traits.
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
GetCandReg(highobj, annot, traits)
GetCisCandReg(highobj, cand.reg, lod.thr = NULL)
GetCoMappingTraits(highobj, cand.reg)
Arguments
highobj |
data frame from |
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 |
cand.reg |
data frame with candidate regulator; see value section below |
lod.thr |
LOD threshold; restrict to intervals above this value if
not |
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 |
Author(s)
Elias Chaibub Neto
References
Manichaikul et al. (2006) Genetics
See Also
Examples
## 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)