qSIP_bootstrap: Calculate bootstrap CI for atom fraction excess using q-SIP...

In nick-youngblut/HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

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)

nick-youngblut/HTSSIP documentation built on May 23, 2019, 4:46 p.m.