qPCR_sim: Simulate qPCR values

In HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

Description

qPCR values will be simulated for each sample in the provided phyloseq object. The error distribution for each sample is drawn from a Gaussian distribution, where the mean and standard deviation of the Gaussian distribution are set by user-defined functions. The user-defined functions that take buoyant density as input and returns a numeric value (see examples), which allows the qPCR values to increase in mean & variance at certain buoyant densities.

Usage

qPCR_sim(physeq, control_mean_fun, control_sd_fun, treat_mean_fun,
  treat_sd_fun, n_tech_rep = 3, control_expr = NULL)

Arguments

physeq	Object of class "phyloseq"
control_mean_fun	Function used for simulating the qPCR normal distribution mean for control samples.
control_sd_fun	Function used for simulating the qPCR normal distribution standard deviation for control samples.
treat_mean_fun	Function used for simulating the qPCR normal distribution mean for treatment samples.
treat_sd_fun	Function used for simulating the qPCR normal distribution standard deviation for treatment samples.
n_tech_rep	Number of technical replicates.
control_expr	Expression used to identify control samples based on sample_data.

Value

data.frame of qPCR values

Examples

# making functions for simulating values
## 'x' will be Buoyant_density as defined in the phyloseq object sample_data
control_mean_fun = function(x) dnorm(x, mean=1.70, sd=0.01) * 1e8
## This will set sd to scale with the mean
control_sd_fun = function(x) control_mean_fun(x) / 3
## This will 'shift' the gene copy distribution to 'heavier' BDs
treat_mean_fun = function(x) dnorm(x, mean=1.75, sd=0.01) * 1e8
treat_sd_fun = function(x) treat_mean_fun(x) / 3
# simulating qPCR values
df_qPCR = qPCR_sim(physeq_S2D2,
                control_expr='Substrate=="12C-Con"',
                control_mean_fun=control_mean_fun,
                control_sd_fun=control_sd_fun,
                treat_mean_fun=treat_mean_fun,
                treat_sd_fun=treat_sd_fun)

# using the Cauchy distribution instead of normal distributions
control_mean_fun = function(x) dcauchy(x, location=1.70, scale=0.01) * 1e8
control_sd_fun = function(x) control_mean_fun(x) / 3
treat_mean_fun = function(x) dcauchy(x, location=1.74, scale=0.01) * 1e8
treat_sd_fun = function(x) treat_mean_fun(x) / 3
# simulating qPCR values
df_qPCR = qPCR_sim(physeq_S2D2,
                control_expr='Substrate=="12C-Con"',
                control_mean_fun=control_mean_fun,
                control_sd_fun=control_sd_fun,
                treat_mean_fun=treat_mean_fun,
                treat_sd_fun=treat_sd_fun)

HTSSIP documentation built on Sept. 14, 2019, 1:02 a.m.