qSIP_bootstrap_fcr: Calculate adjusted bootstrap CI after for multiple testing...

In SIPmg: Statistical Analysis to Identify Isotope Incorporating MAGs

Calculate adjusted bootstrap CI after for multiple testing for atom fraction excess using q-SIP method. Multiple hypothesis tests are corrected by

Description

Calculate adjusted bootstrap CI after for multiple testing for atom fraction excess using q-SIP method. Multiple hypothesis tests are corrected by

Usage

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

Arguments

atomX	A list object created by qSIP_atom_excess_MAGs()
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.
ci_adjust_method	Confidence interval adjustment method. Please choose 'FCR', 'Bonferroni', or 'none' (if no adjustment is needed). Default is FCR and also provides unadjusted CI.
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 adjusted for multiple testing.

Examples

data(phylo.qSIP,GC_content)

### BD shift (Z) & atom excess (A)
atomX = qSIP_atom_excess_MAGs(phylo.qSIP,
                        control_expr='Isotope=="12C"',
                        treatment_rep='Replicate', Gi = GC_content)

### Add doParallel::registerDoParallel(num_cores) if parallel bootstrapping is to be done
df_atomX_boot = qSIP_bootstrap_fcr(atomX, n_boot=5, parallel = FALSE)

SIPmg documentation built on March 7, 2023, 6:47 p.m.