map.index {bqtl} | R Documentation |
One way to index a locus (loci) in a genetic map is by the numerical index of
its row (their rows). map.index
performs a lookup in a specific
map.frame
given one (or two) chromosome number(s) and one (or
two) map distance(s).
map.index(x, ... )
x |
A |
... |
For methods that look up a location in a |
It is often convenient to refer to genetic loci or regions by the
numerical index(es) in a map.frame
. map.index
allows
lookups according to the approximate map location.
A numerical vector of one or more row numbers. If only chromo
is
specified, all row numbers on the specified chromosome are returned. If
chromo
has two elements, then all row numbers on those
chromosomes with numbers in range(chromo)
will be returned. If
one of each of chromo
and cM
are specified, then the row
number of the closest locus will be returned. For two of each, row
numbers in the range of the closest matches will be returned.
Charles C. Berry cberry@ucsd.edu
make.map.frame
for a description of how map
information is organized.
data(little.ana.bc)
map.index(little.ana.bc,chromo=1,cM=25) # locus nearest 1,25
index.chr.1 <- map.index(little.ana.bc,chromo=1)
fit.on.1 <- bqtl(bc.phenotype~locus(index.chr.1),little.ana.bc)
summary( loglik( fit.on.1 ) )