stack3 {rseedcalc}

Multinomial group testing estimation of stacked genes

Description

Assuming qualitative tests are performed on n pools of m seeds, use multinomial group testing to estimate the percent of seeds with single genetic traits and the percentage of seeds with stacked genetic traits.

Print method for seedstack object.

Usage

stack3(n, m, nA, nB, nC, nAB, nAC, nBC, nABC, existAB = "Yes",
  existAC = "Yes", existBC = "Yes", existABC = "Yes", fpr = 0,
  fnr = 0, check = TRUE)

stack2Excel(...)

stack3Excel(...)

stack2(n, m, nA, nB, nAB, existAB = "Yes", fpr = 0, fnr = 0,
  check = TRUE)

## S3 method for class 'seedstack'
print(x, ...)

Arguments

n

the number of pools

m

the number of seeds in each pool

nA

the number of positive pools for event A only

nB

the number of positive pools for event B only

nAB

the number of positive pools for both A and B

nC

the number of positive pools for event C only

nAC

the number of positive pools for both A and C

nBC

the number of positive pools for both B and C

nABC

the number of positive pools for both A and B and C

existAB

do seeds with a stacked event 'AB' exist?

existAC

do seeds with a stacked event 'AC' exist?

existBC

do seeds with a stacked event 'BC' exist?

existABC

do seeds with a stacked event 'ABC' exist?

fpr

false positive rate (proportion) for detecting GM events

fnr

false negative rate (proportion) for detecting GM events

check

Should simple checks be performed? Defaults to TRUE

...

Other arguments passed

x

A data frame to print pretty.

Details

The 'stack2Excel' and 'stack3Excel' functions are simple wrappers that are intended to be called from Excel and should not issue any warnings.

Value

A data frame with the estimated proportion of seeds for each event, the observed and expected number of positive pools, and whether or not each event can exist.

Author(s)

Kevin Wright, Jean-Louis Laffont

Examples

stack2(10, 300, 0, 1, 2)
stack3(20,150, 2,2,2,2,2,2,3, existAB="no", fnr=.02, fpr=.02)