digitalPCR (version 1.0)

digitalPCR: Estimate copy number and assay sensitivity from dPCR serial dilution

Description

The assay sensitivity is the minimum number of copies that the digital PCR assay can detect. Users provide serial dilution results in the format of counts of positive and total reaction wells. The output is the estimated assay sensitivity and the copy number per well in the initial dilute.

Usage

digitalPCR(pos, n, dilution, Nboot, single.copy = c("FALSE", "TRUE"))

Arguments

pos

a numeric vector of number of positive reactions in the order of dilutions

n

a number or a numeric vector of number of total reactions in the order of dilutions

dilution

a numeric vector of folds of dilutions relative to the initial dilution

Nboot

number of bootstrapping

single.copy

character tells whether the assay is assumed single-copy sensitive. default "FALSE"

Value

• The returned value is a list of four components:
• mean copy number
  mean copy number
• sd copy number
  standard deviation of copy number
• copy numbers
  bootstrapped copy number estimates
• thresholds
  bootstrapped assay sensitivity estimates

Details

The total number n can be a vector or a number which will be recycled. If the assay is assumed single-copy sensitive, single.copy can be set to "TRUE". If the assay contains 3 dilutions at 1, 2, and 4 fold relative to initial concentrate, set dilution=c(1,2,4)

Examples

#dilution at 1,2,4,8 fold
pos=c(221,97,39,14)
dilution=c(1,2,4,8)
n=384
#note in practice, set this 100 or larger
Nboot=10 

result1=digitalPCR(pos, n, dilution,  Nboot)
print (paste(result1$"mean copy number", result1$"sd copy number"))
hist(result1$"thresholds",xlim=c(-2,10))

#the following example contains only 1 dilution
result2=digitalPCR(230, 355, 1,  Nboot, "TRUE")