addMissing: Adds missing data to objects of class autoMarker or autoCross

In polySegratio: Simulate and Test Marker Dosage for Dominant Markers in Autopolyploids

Description

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.

Usage

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

Value

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 [e-mail]

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)

polySegratio documentation built on May 2, 2019, 7:26 a.m.