frederickhuanglin / ancom-bc-code-archive

Archive: Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction". Please check our ANCOMBC R package for the most up-to-date ANCOM-BC function.

User Manual for ANCOM-BC Function

This is the repository archiving data and scripts for reproducing results presented in the Nat. Comm. paper ANCOM-BC.

For the corresponding R package, refer to ANCOMBC repository.

The current code implements ANCOM-BC in cross-sectional datasets for comparing the change of absolute abundance for each taxon among different experimental groups.

R-package dependencies

The following libraries need to be included for the R code to run:

library(dplyr)
library(nloptr)

Instructions for use

Data preprocess

Usage

• feature_table_pre_process(feature.table, meta.data, sample.var, group.var, zero.cut, lib.cut, neg.lb)

Arguments

• feature.table: Data frame or matrix representing observed OTU table with OTUs (or taxa) in rows and samples in columns.
• meta.data: Data frame or matrix of all variables and covariates of interest.
• sample.var: Character. The name of column storing sample IDs.
• group.var: Character. The name of the main variable of interest. ANCOM-BC v1.0 only supports discrete group.var and aims to compare the change of absolute abundance across different levels of group.var.
• zero.cut: Numerical fraction between 0 and 1. Taxa with proportion of zeroes greater than zero.cut are not included in the analysis.
• lib.cut: Numeric. Samples with library size less than lib.cut are not included in the analysis.
• neg.lb: Logical. TRUE indicates a taxon would be classified as a structural zero in the corresponding experimental group using its asymptotic lower bound.

Value

• feature.table: A data frame of pre-processed OTU table.
• library.size: A numeric vector of library sizes after pre-processing.
• group.name: A character vector of levels of group.var.
• group.ind: A numeric vector. Each sample is assigned to a number indicating its group label for better internal process.
• structure.zeros: A matrix consists of 0 and 1s with 1 indicating the taxon is identified as a structural zero in the corresponding group.

ANCOM-BC main function

Usage:

• ANCOM_BC(feature.table, grp.name, grp.ind, struc.zero, adj.method, tol.EM, max.iterNum, perNum, alpha)

Arguments:

• feature.table: Data frame or matrix representing the pre-processed OTU table with OTUs (or taxa) in rows and samples in columns.
• grp.name: A character vector indicating the levels of group.
• grp.ind: A numeric vector indicating group assignment for each sample. 1 corresponds to the 1st level of grp.name, 2 corresponds to the 2nd level of grp.name, etc.
• struc.zero: A matrix consists of 0 and 1s with 1 indicating the taxon is identified as a structural zero in the corresponding group.
• adj.method: Character. Returns p-values adjusted using the specified method, including "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".
• tol.EM: Numeric. The iteration convergence tolerance for E-M algorithm.
• max.iterNum: Numeric. The maximum number of iterations for E-M algorithm.
• perNum: Numeric. The maximum number of permutations. This argument is active only if there exist more than 2 groups.
• alpha: Numeric. Level of significance.

Value:

• feature.table: Data frame or matrix. Return the input feature.table.
• res: Data frame. The primary result of ANCOM-BC consisting of:
  • mean.difference: Numeric. The estimated mean difference of absolute abundance between groups in log scale (natural log);
  • se: Numeric. The standard error of mean.difference;
  • W: Numeric. mean.difference/se, which is the test statistic of ANCOM-BC.
  • p.val: Numeric. P-value obtained from two-sided Z-test using the test statistic W.
  • q.val. Numeric. Q-value obtained by applying adj.method to p-val.
  • diff.abn. Logical. TRUE if the taxon has q.val less than alpha.
• d: A numeric vector. Estimated sampling fractions in log scale (natural log).
• mu: A numeric vector. Estimated log (natural log) mean absolute abundance for each group.
• bias.em: Numeric. Estimated mean difference of log (natural log) sampling fractions between groups through E-M algorithm.
• bias.wls: Numeric. Estimated mean difference of log (natural log) sampling fractions between groups through weighted least squares.

Flowchart of ANCOM-BC

Examples

# Load example data
data(dietswap)
pseq = dietswap
n_taxa = ntaxa(pseq)
n_samp = nsamples(pseq)
# Metadata
meta_data = meta(pseq)
# Taxonomy table
taxonomy = tax_table(pseq)
# Absolute abundances
otu_absolute = abundances(pseq)

Two-group comparison

# Pre-processing
feature.table = otu_absolute; sample.var = "sample"; group.var = "nationality"; 
zero.cut = 0.90; lib.cut = 1000; neg.lb = TRUE
pre.process = feature_table_pre_process(feature.table, meta_data, sample.var, 
                                        group.var, zero.cut, lib.cut, neg.lb)
feature.table = pre.process$feature.table
group.name = pre.process$group.name
group.ind = pre.process$group.ind
struc.zero = pre.process$structure.zeros

# Paras for ANCOM-BC
grp.name = group.name; grp.ind = group.ind; adj.method = "bonferroni"
tol.EM = 1e-5; max.iterNum = 100; perNum = 1000; alpha = 0.05

out = ANCOM_BC(feature.table, grp.name, grp.ind, struc.zero,
               adj.method, tol.EM, max.iterNum, perNum, alpha)
res = cbind(taxon = rownames(out$feature.table), out$res)
write_csv(res, "demo_two_group.csv")

Expected run time: 6s (R version 3.5.1 (2018-07-02); Platform: x86_64-apple-darwin15.6.0 (64-bit); Running under: macOS 10.15.1.)

Multi-group comparison

# Pre-processing
feature.table = otu_absolute; sample.var = "sample"; group.var = "bmi_group"; 
zero.cut = 0.90; lib.cut = 1000; neg.lb = TRUE
pre.process = feature_table_pre_process(feature.table, meta_data, sample.var, 
                                        group.var, zero.cut, lib.cut, neg.lb)
feature.table = pre.process$feature.table
group.name = pre.process$group.name
group.ind = pre.process$group.ind
struc.zero = pre.process$structure.zeros

# Paras for ANCOM-BC
grp.name = group.name; grp.ind = group.ind; adj.method = "bonferroni"
tol.EM = 1e-5; max.iterNum = 100; perNum = 1000; alpha = 0.05

out = ANCOM_BC(feature.table, grp.name, grp.ind, struc.zero,
               adj.method, tol.EM, max.iterNum, perNum, alpha)
res = cbind(taxon = rownames(out$feature.table), out$res)
write_csv(res, "demo_multi_group.csv")

Expected run time: 19s (R version 3.5.1 (2018-07-02); Platform: x86_64-apple-darwin15.6.0 (64-bit); Running under: macOS 10.15.1.)