stack2 function

Multinomial group testing estimation of stacked genes

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.

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.

Returns

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.

Details

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

Examples

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

Author(s)

Kevin Wright, Jean-Louis Laffont