addMissing function

Adds missing data to objects of class autoMarker or autoCross

Adds missing data to objects of class simAutoMarkers or simAutoCross as specified either as a proportion of missing at random or a proportion of columns and rows with specified proportions of missings.

addMissing(x, na.proportion = 0, parent.cols = c(1, 2), seed)

Arguments

• x: object of class simAutoMarkers or simAutoCross, or a matrix with dominant markers scored as 0 or 1
• na.proportion: proportion missing at random or a list with two components indiv and marker each containing c(prop. markers missing, prop. missing) (Default: 0)
• parent.cols: columns containing parental markers (etc) not altered only used if object of class simAutoCross
• seed: random number generator (RNG) state for random number which will be set at start to reproduce results

Returns

Returns object of class simAutoMarkers or simAutoCross, or a matrix with dominant markers scored as 0 or 1 with extra component na.proportion which has the following elements - na.proportion: proportion missing at random or a list with two components indiv and marker each containing c(prop. markers missing, prop. missing)

• time.generated: time/date when data set generated + when missing added

• seed: random number generator seed which could be used to reproduce results (I hope)

• call: matches arguments when function called

Author(s)

Peter Baker p.baker1@uq.edu.au

See Also

addMisclass misclassifies 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 missings
addMissing(p2, 0.1)