addMisclass {polySegratio} | R Documentation |
Misclassifies marker data in objects of class autoMarker or autoCross
Description
Marker data are misclassified at a specified rate for objects
of class simAutoMarkers
or simAutoCross
. The rate may be
specified either as a proportion of missing at random or a proportion
of columns and rows with specified proportions of missings.
Usage
addMisclass(x, misclass = 0, bands.missed=0, parents = FALSE,
parent.cols = c(1, 2), seed)
Arguments
x |
object of class |
misclass |
proportion misclassified specified as for na.proportion (Default: 0) |
bands.missed |
proportion of bands that are not scored when they are actually present. Note this is applied to correctly specified markers after markers are misclassified (Default: 0) |
parents |
if TRUE then misclassify parental alleles, otherwise misclassify offspring marker alleles |
parent.cols |
for object of simAutoClass the columns containg parental markers |
seed |
random number generator (RNG) state for random number which will be set at start to reproduce results |
Value
returns object of class simAutoMarkers
or simAutoCross
,
or a matrix with
dominant markers scored as 0 or 1 with extra components
misclass.info |
list with components
|
Author(s)
Peter Baker p.baker1@uq.edu.au
See Also
addMissing
add missing markers at random,
sim.autoMarkers
simulate autopolyploid markers,
sim.autoCross
simulate autopolyploid markers for a cross
Examples
## simulate autopolyploid markers
p1 <- sim.autoCross(4, dose.proportion=c(0.7,0.3), n.markers=20, n.indiv=10)
p2 <- sim.autoCross(4, dose.proportion=list(p01=c(0.7,0.3),p10=c(0.7,0.3),p11=c(
0.6,0.2,0.2)))
## add misclassified for a whopping 20% of markers
print(addMisclass(p1, 0.2, parents=TRUE), row=1:20)
addMisclass(p2, 0.1)