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.
make.map.frame(dx,chr.num = NULL, prior = make.location.prior(lambda),
morgan = 100, nint = NULL, reso = NULL)
A data frame with components:
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.
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
.
"left" if it is the first locus on this chromosome,"right" if it is last, or "center" otherwise.
TRUE if this was actually a marker, FALSE if it is a 'virtual' marker
Plotting position for this locus. Typically the same as
dx
.
Twice the recombination fraction minus one.
An abbreviation for the locus of the form
"C.<chr.num
>.<cM
>"
The chromosome number.
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 centiMorgans (from start of
chromosome or Morgans if M
was the column name). It is best
if names(dx)
(for vector arguments)
or row.names(dx)
(for data.frame arguments) give names of
markers for later reference, but this isn't really necessary.
(Optional) Vector of chromosome numbers
(Optional) Vector of Prior probabilities for the loci
100 if centiMorgans, 1 if Morgans
(Optional) Vector of one plus number of 'virtual' markers to be inserted after each locus
Maximum distance between loci. If necessary fill in with 'pseudo-markers'
Charles C. Berry cberry@ucsd.edu
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.
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
rm( little.map.dx,little.map.frame ,little.mf.5)
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