make.map.frame: Create marker map specifications

Description Usage Arguments Details Value Note Author(s) Examples

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

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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 cberry@ucsd.edu

Examples

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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 May 2, 2019, 10:19 a.m.

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