compare: Difference comparison

In microbiota/amplicon: Statistics and visualization for microbiome data

Difference comparison

Description

Input feature table, group info and comparing pair Features with relative abundance, p-value and FDR for pair.

Usage

compare(
  data = otutab,
  metadata = metadata,
  group = "Group",
  compare_pair = "KO-WT",
  method = "wilcox",
  RA = 0.01,
  pvalue = 0.05,
  fdr = 0.1,
  normalize = T
)

Arguments

data	data matrix
metadata	matrix or dataframe, including sampleID and groupID;
group	column name for groupID.
compare_pair	paired groups linked with dash.
method	method of test.
RA	threshold for relative abundance.
pvalue	threshold of pvalue.
fdr	threshold of fdr.
normalize	data normalize to 100%, default T, turn off by F.

Details

By default, return table The available test methods include the following:

• most used methods: wilcoxon test, t.test

• other used indices: edgeR, DESeq2

Value

Difference comparison table.

Author(s)

Contact: Yong-Xin Liu [e-mail]

References

Yong-Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo & Yang Bai. A practical guide to amplicon and metagenomic analysis of microbiome data. Protein Cell, 2020(41), 1-16, DOI: https://doi.org/10.1007/s13238-020-00724-8

See Also

compare_vocalno compare_heatmap compare_manhattan

Examples

# Table, metadata, groupID, compare pair and method (wilcoxon test)
compare(data = otutab, metadata = metadata, group = "Group", compare_pair = "KO-WT", method = "wilcox")
# Filter by 0.01% relative abundance, Pvalue and FDR, not normalize
compare(data = otutab, metadata = metadata, group = "Group", compare_pair = "KO-WT", method = "wilcox", RA = 0.01, pvalue = 0.05, fdr = 0.1, normalize = F)

microbiota/amplicon documentation built on April 30, 2023, 1:48 p.m.