bqtl (version 1.0-7)

map.location: Report map location

Description

Report the chromosome number and location of loci in a genetic map.

Usage

map.location(x,...)
map.loc(x, ...)

Arguments

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

Value

• 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

Details

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.

See Also

make.map.frame

Examples

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)