simPCR: PCR Simulator

In pcrsim: Simulation of the Forensic DNA Process

Description

Simulates the Polymerase Chain Reaction (PCR) process.

Usage

simPCR(data, kit = NULL, method = "DEFAULT", pcr.cyc = 30,
  pcr.prob = 0.8, sd.pcr.prob = 0, stutter = TRUE, stutter.prob = 0.002,
  sd.stutter.prob = 0, stutter.reg = FALSE, vol.aliq = 10,
  sd.vol.aliq = 0, vol.pcr = 25, sd.vol.pcr = 0, debug = FALSE)

Arguments

data	data.frame with simulated data. Preferably output from simExtraction. Required columns are 'Marker', 'Allele', 'Sim', Volume', and 'DNA'.
kit	string representing the typing kit used, or data.frame with kit characteristics. Provides locus specific PCR efficiency and stutter probabilities. If NULL pcr.prob and stutter.prob will be used for all loci.
method	string representing the method of the specified kit.
pcr.cyc	numeric for the number of PCR cycles.
pcr.prob	numeric for the PCR efficiency (probability amplifying a DNA molecule). Only used if kit is NULL.
sd.pcr.prob	numeric for the standard deviation of pcr.prob.
stutter	logical to simulate stutters.
stutter.prob	numeric for the probability generating a stutter. Only used if kit is NULL.
sd.stutter.prob	numeric for the standard deviation of stutter.prob.
stutter.reg	logical to use regression for stutter probability.
vol.aliq	numeric for the aliquot extract forwarded to PCR.
sd.vol.aliq	numeric for the standard deviation of vol.aliq.
vol.pcr	numeric for the total PCR reaction volume.
sd.vol.pcr	numeric for the standard deviation of vol.pcr.
debug	logical to print debug information.

Details

Simulates the PCR process by a series of binomial distributions, or multinomial distributions if stutter=TRUE. The PCR probability/ efficiency can be specified globally or per locus. Probability of stutter formation can be specified globally, per locus, or per locus and allele size.

Value

data.frame with simulation results in columns 'PCR.Pip.Vol', 'PCR.Aliq.Prob', 'PCR.DNA', 'PCR.Vol', 'PCR.Prob', 'PCR.Prob.Stutter', 'PCR.Amplicon', 'PCR.Stutter.1', 'PCR.Stutter.2', and updated 'DNA' column (added if needed).

See Also

simExtraction

Examples

# Create a data frame with a DNA profile.
markers = rep(c("D3S1358","TH01","FGA"), each=2)
alleles = c(15,18,6,10,25,25)
df <- data.frame(Marker=markers, Allele=alleles)

# Simulate profile.
smpl <- simProfile(data=df, sim=10)

# Simulate sample.
smpl <- simSample(data=smpl, cells=1000, sd.cells=200)

# Simulate extraction.
smpl <- simExtraction(data=smpl, vol.ex=200, sd.vol=10, prob.ex=0.6, sd.prob=0.1)

# Simulate PCR with 95% PCR efficiency and 0.2% stutter probability for all loci.
res <- simPCR(data=smpl, pcr.prob=0.95, pcr.cyc=30, vol.aliq=10,
 sd.vol.aliq=0.1, vol.pcr=25, sd.vol.pcr=1)

# Simulate PCR with locus specific PCR efficiency and stutter probability.
res <- simPCR(data=smpl, kit="ESX17", pcr.cyc=30, vol.aliq=10,
 sd.vol.aliq=0.1, vol.pcr=25, sd.vol.pcr=1)

# Simulate PCR with locus specific PCR efficiency and stutter probability.
res <- simPCR(data=smpl, kit="ESX17", pcr.cyc=30, vol.aliq=10,
 sd.vol.aliq=0.1, vol.pcr=25, sd.vol.pcr=1, stutter.reg=TRUE)

Example output

Loading required package: strvalidator
R session is headless; GTK+ not initialized.
STR-validator 2.0.0 loaded!
PCRsim 1.0.2 loaded!
SIMULATE PROFILE
'Sim' column added.
'Sample.Name' column added.
SIMULATE SAMPLE
'Sample.Haploid' column added.
'Sample.Cells' column added.
'DNA' column added.
SIMULATE EXTRACTION
'Ex.Vol' column added.
'Ex.Prob' column added.
'Ex.DNA' column added.
'Ex.Conc' column added.
'Volume' column added.
'DNA' column updated!
SIMULATE POLYMERASE CHAIN REACTION
'PCR.Pip.Vol' column added
'PCR.Aliq.Prob' column added
'PCR.DNA' column added.
'PCR.Vol' column added.
'kit' is not provided. Using PCR probability on a per sample basis.
'PCR.Prob' column added.
'PCR.Prob.Stutter' column added.
Sum probabilities check passed (<=1).
'PCR.Amplicon' column added.
'PCR.Stutter.1' column added.
'PCR.Stutter.2' column added.
'DNA' column updated!
SIMULATE POLYMERASE CHAIN REACTION
'PCR.Pip.Vol' column added
'PCR.Aliq.Prob' column added
'PCR.DNA' column added.
'PCR.Vol' column added.
'kit' is provided. Using PCR probability on a per locus basis.
Fetch kit parameters from file.
'PCR.Prob' column added.
'PCR.Prob.Stutter' column added.
Use fixed values for stutter probability.
Sum probabilities check passed (<=1).
'PCR.Amplicon' column added.
'PCR.Stutter.1' column added.
'PCR.Stutter.2' column added.
'DNA' column updated!
'Allele' must be character. 'data' converted
Audit trail created for data in function strvalidator::addSize.
Audit trail updated by function strvalidator::addSize.
Added column 'Size'
SIMULATE POLYMERASE CHAIN REACTION
'PCR.Pip.Vol' column added
'PCR.Aliq.Prob' column added
'PCR.DNA' column added.
'PCR.Vol' column added.
'kit' is provided. Using PCR probability on a per locus basis.
Fetch kit parameters from file.
'PCR.Prob' column added.
'PCR.Prob.Stutter' column added.
Use regression to calculate stutter probability.
Sum probabilities check passed (<=1).
'PCR.Amplicon' column added.
'PCR.Stutter.1' column added.
'PCR.Stutter.2' column added.
'DNA' column updated!

pcrsim documentation built on May 2, 2019, 2:40 a.m.