Usage
select.markers.for.pairscan(data.obj, geno.obj = NULL,
singlescan.obj, alpha.thresh = NULL,
t.thresh = NULL, specific.markers = NULL,
num.markers = NULL, step.size = NULL,
tolerance = 10, verbose = TRUE)
Arguments
geno.obj
The object in which the genotype data is stored. See read.geno.
singlescan.obj
The object in which results from singlescan are stored.
alpha.thresh
A numeric threshold for selecting markers based on significance at the given alpha value.
t.thresh
A numerical value indicating a standardized effect size below which markers are rejected for the pair scan.
specific.markers
An optional vector of column numbers or names specifying specific markers to include in the pairscan.
num.markers
An optional number. If specified, the algorithm attempts to find a standardized effect threshold that will give the number of markers specified. This can take a long time, since linear non-independence must be calculated for each thresholded set of markers.
step.size
If num.markers is specified, this argument determines how the t.thresh is changed when searching for markers to include in the pairscan.
tolerance
If num.markers is specified, tolerance determines how close the algorithm will get to the number of desired markers. If 100 markers are desired, and tolerance is set to 10, the algorithm will stop if it finds a threshold giving between 90 and 110 markers.
verbose
A logical value indicating whether the progress of the threshold finding algorithm should be reported.