make.map.frame: Create marker map specifications

In bqtl: Bayesian QTL Mapping Toolkit

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 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.
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'

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.

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.

Note

The idea in having all of this bundled together is to make it easier for plot and summary methods to be implemented and to allow convenient references in formula based methods.

Author(s)

Charles C. Berry [e-mail]

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

bqtl documentation built on Sept. 25, 2024, 1:08 a.m.