findDupMarkers {qtl}

Find markers with identical genotype data

Description

Identify sets of markers with identical genotype data.

Usage

findDupMarkers(cross, chr, exact.only=TRUE, adjacent.only=FALSE)

Arguments

cross

An object of class cross. See read.cross for details.

chr

Optional vector specifying which chromosomes to consider. This may be a logical, numeric, or character string vector.

exact.only

If TRUE, look only for markers that have matching genotypes and the same pattern of missing data; if FALSE, also look for cases where the observed genotypes at one marker match those at another, and where the first marker has missing genotype whenever the genotype for the second marker is missing.

adjacent.only

If TRUE, look only for sets of markers that are adjacent to each other.

Details

If exact.only=TRUE, we look only for groups of markers whose pattern of missing data and observed genotypes match exactly. One marker (chosen at random) is selected as the name of the group (in the output of the function).

If exact.only=FALSE, we look also for markers whose observed genotypes are contained in the observed genotypes of another marker. We use a pair of nested loops, working from the markers with the most observed genotypes to the markers with the fewest observed genotypes.

Value

A list of marker names; each component is a set of markers whose genotypes match one other marker, and the name of the component is the name of the marker that they match.

Author(s)

Karl W Broman, [e-mail]

See Also

drop.nullmarkers, drop.markers, pickMarkerSubset

Examples

data(hyper)

hyper <- drop.nullmarkers(hyper)

dupmar <- findDupMarkers(hyper) # finds 4 pairs
dupmar.adjonly <- findDupMarkers(hyper, adjacent.only=TRUE) # finds 4 pairs

dupmar.nexact <- findDupMarkers(hyper, exact.only=FALSE, adjacent.only=TRUE) # finds 6 pairs

# one might consider dropping the extra markers
totmar(hyper) # 173 markers
hyper <- drop.markers(hyper, unlist(dupmar.adjonly))
totmar(hyper) # 169 markers