bqtl (version 1.0-7)

make.map.frame: Create marker map specifications

Description

A map.frame.object describes a marker map and additional loci that may be used in a QTL study. Each row pertains to one locus. Names of markers, abbreviated names, distances, and other necessary and useful information are bundled.

Usage

make.map.frame(dx,chr.num = NULL, prior = make.location.prior(lambda), 
    morgan = 100, nint = NULL, reso = NULL)

Arguments

dx

An object of class "map.frame" or class "data.frame" or a vector or a data.frame with a column named cM, M, or dx or whose first column gives location on each chromosome in ce

chr.num

(Optional) Vector of chromosome numbers

prior

(Optional) Vector of Prior probabilities for the loci

morgan

100 if centiMorgans, 1 if Morgans

nint

(Optional) Vector of one plus number of 'virtual' markers to be inserted after each locus

reso

Maximum distance between loci. If necessary fill in with 'pseudo-markers'

Value

• A data frame with components:
• marker.name
  The full text identifier for this marker, e.g. "HH.360L.Col" is a marker on chromosome 1 of arabidopsis thaliana, and names like this can be used for reference purposes. 'Virtual' markers have a suffix appended to the name of the previous marker.
• cM
  Location on the chromosome. If this is a marker of a locus that was input via dx, then it is just the value of dx.
• pos.type
  "left" if it is the first locus on this chromosome,"right" if it is last, or "center" otherwise.
• is.marker
  TRUE if this was actually a marker, FALSE if it is a 'virtual' marker
• pos.plot
  Plotting position for this locus. Typically the same as dx.
• lambda
  Twice the recombination fraction minus one.
• locus
  An abbreviation for the locus of the form "C.<chr.num>.<cM>"
• chr.num
  The chromosome number.

Details

The QTL analysis depends on information about the marker map and on specifications of the loci to be studied. The 'map.frame' contains this information.

Examples

data( little.map.dx )
little.map.frame <- make.map.frame( little.map.dx )
plot( little.map.frame ) # there is a plot method
# add 'virtual' markers to map
little.mf.5 <-   make.map.frame(little.map.frame,reso=5)
print(little.mf.5[1:10,],digits=1) # show a few rows
plot( little.mf.5 ) # notice the 'virtual' markers added
<testonly>rm( little.map.dx,little.map.frame ,little.mf.5)</testonly>