SIPmg (version 3.0)

qSIP_bootstrap_fcr: 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,
  n_sample = c(3, 3),
  ci_adjust_method = "fcr",
  n_boot = 10,
  parallel = FALSE,
  a = 0.1,
  Gi,
  show_delbd_AFE = FALSE
)

Value

A data.frame of atom fraction excess values (A) and atom fraction excess confidence intervals adjusted for multiple testing.

Arguments

atomX

A list object created by qSIP_atom_excess_MAGs()

isotope

The isotope for which the DNA is labeled with ('13C', '15N' 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.

Gi

The G+C content of unlabeled DNA as a dataframe with "Feature" column having MAGs, contigs, or other features as rows, and a "Gi" column with GC content

show_delbd_AFE

Show AFE values and incorporator identification estimated based on the delta buoyant density estimates?

Examples

data(phylo.qSIP,GC_content)
# \donttest{
### 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, isotope = "13C", Gi = GC_content,
                                   n_boot=5, parallel = FALSE)
# }