| map.location {bqtl} | R Documentation |
Report the chromosome number and location of loci in a genetic map.
map.location(x,... ) map.loc(x, ... )
x |
A object of class map.frame,analysis.object,
bqtl, or bqtl.list |
... |
Other arguments usage depend on the class of x :
y{A vector of row numbers or map.names specifying which
subset of the map.frame of x is to be returned}
chromo{A vector of chromosome numbers}
cM {(Optional) map distance vector. If the same chromosome
number is used twice in chromo, cM must be
ordered. If cM is omitted, all loci on each chromosome listed
in chromo will be included.}
map.names{A vector of map.names}
|
It is often helpful to refer to genentic loci by their
locations. The methods of map.location (alias map.loc)
will extract the row index, chromosome number and location, and the name
for specified loci. For direct lookups of the loci in a map.frame
or analysis.object, one must specify y or chromo or
map.names. When class(x)=="bqtl" map.locations of
terms used in a call to bqtl are returned. When cM is
used, an attempt will be made to match the location; if the match fails,
the nearest locus will be used. When there are two elements in
chromo and two in cM, all the map locations in between the
matching loci will be returned.
An object of class map.location which inherits from
map.frame. It has columns:
chr.num |
The chromosome number |
cM |
The location in centiMorgans on that chromosome. |
marker.name |
The name by which that marker is known |
attr(,"row.names") |
An index of the locations |
Charles C. Berry cberry@ucsd.edu
data(little.ana.bc) map.loc(little.ana.bc, c(1,15,45)) map.loc(little.ana.bc,chromo=3,cM=22) map.loc(little.ana.bc,"m.12") rm(little.ana.bc)