qSIP_bootstrap {HTSSIP}

Calculate bootstrap CI for atom fraction excess using q-SIP method

Description

Calculate bootstrap CI for atom fraction excess using q-SIP method

Usage

qSIP_bootstrap(atomX, isotope = "13C", n_sample = c(3, 3),
  n_boot = 10, parallel = FALSE, a = 0.1)

Arguments

atomX

A list object created by qSIP_atom_excess()

isotope

The isotope for which the DNA is labeled with ('13C' or '18O')

n_sample

A vector of length 2. The sample size for data resampling (with replacement) for 1) control samples and 2) treatment samples.

n_boot

Number of bootstrap replicates.

parallel

Parallel processing. See .parallel option in dplyr::mdply() for more details.

a

A numeric value. The alpha for calculating confidence intervals.

Value

A data.frame of atom fraction excess values (A) and atom fraction excess confidence intervals.

Examples

# tranforming values
physeq_rep3_t = OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR)

## Not run: 
# BD shift (Z) & atom excess (A)
atomX = qSIP_atom_excess(physeq_rep3_t,
                        control_expr='Treatment=="12C-Con"',
                        treatment_rep='Replicate')

# bootstrapping in parallel
doParallel::registerDoParallel(2)
df_atomX_boot = qSIP_bootstrap(atomX, parallel=TRUE)
head(df_atomX_boot)

## End(Not run)