run_edger: Perform differential analysis using edgeR

In HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics

Perform differential analysis using edgeR

Description

Differential expression analysis based on the Negative Binomial distribution using edgeR.

Usage

run_edger(
  ps,
  group,
  confounders = character(0),
  contrast = NULL,
  taxa_rank = "all",
  method = c("LRT", "QLFT"),
  transform = c("identity", "log10", "log10p", "SquareRoot", "CubicRoot", "logit"),
  norm = "TMM",
  norm_para = list(),
  disp_para = list(),
  p_adjust = c("none", "fdr", "bonferroni", "holm", "hochberg", "hommel", "BH", "BY"),
  pvalue_cutoff = 0.05,
  ...
)

Arguments

ps	ps a phyloseq::phyloseq object.
group	character, the variable to set the group, must be one of the var of the sample metadata.
confounders	character vector, the confounding variables to be adjusted. default character(0), indicating no confounding variable.
contrast	this parameter only used for two groups comparison while there are multiple groups. For more please see the following details.
taxa_rank	character to specify taxonomic rank to perform differential analysis on. Should be one of phyloseq::rank_names(phyloseq), or "all" means to summarize the taxa by the top taxa ranks (summarize_taxa(ps, level = rank_names(ps)[1])), or "none" means perform differential analysis on the original taxa (taxa_names(phyloseq), e.g., OTU or ASV).
method	character, used for differential analysis, please see details below for more info.
transform	character, the methods used to transform the microbial abundance. See transform_abundances() for more details. The options include: "identity", return the original data without any transformation (default). "log10", the transformation is log10(object), and if the data contains zeros the transformation is log10(1 + object). "log10p", the transformation is log10(1 + object). "SquareRoot", the transformation is ⁠Square Root⁠. "CubicRoot", the transformation is ⁠Cubic Root⁠. "logit", the transformation is ⁠Zero-inflated Logit Transformation⁠ (Does not work well for microbiome data).
norm	the methods used to normalize the microbial abundance data. See normalize() for more details. Options include: "none": do not normalize. "rarefy": random subsampling counts to the smallest library size in the data set. "TSS": total sum scaling, also referred to as "relative abundance", the abundances were normalized by dividing the corresponding sample library size. "TMM": trimmed mean of m-values. First, a sample is chosen as reference. The scaling factor is then derived using a weighted trimmed mean over the differences of the log-transformed gene-count fold-change between the sample and the reference. "RLE", relative log expression, RLE uses a pseudo-reference calculated using the geometric mean of the gene-specific abundances over all samples. The scaling factors are then calculated as the median of the gene counts ratios between the samples and the reference. "CSS": cumulative sum scaling, calculates scaling factors as the cumulative sum of gene abundances up to a data-derived threshold. "CLR": centered log-ratio normalization. "CPM": pre-sample normalization of the sum of the values to 1e+06.
norm_para	arguments passed to specific normalization methods. Most users will not need to pass any additional arguments here.
disp_para	additional arguments passed to edgeR::estimateDisp() used for dispersions estimation. Most users will not need to pass any additional arguments here.
p_adjust	method for multiple test correction, default none, for more details see stats::p.adjust.
pvalue_cutoff	numeric, p value cutoff, default 0.05
...	extra arguments passed to the model. See edgeR::glmQLFit() and edgeR::glmFit() for more details.

Details

Note that edgeR is designed to work with actual counts. This means that transformation is not required in any way before inputting them to edgeR.

There are two test methods for differential analysis in edgeR, likelihood ratio test (LRT) and quasi-likelihood F-test (QLFT). The QLFT method is recommended as it allows stricter error rate control by accounting for the uncertainty in dispersion estimation.

contrast must be a two length character or NULL (default). It is only required to set manually for two groups comparison when there are multiple groups. The order determines the direction of comparison, the first element is used to specify the reference group (control). This means that, the first element is the denominator for the fold change, and the second element is used as baseline (numerator for fold change). Otherwise, users do required to concern this parameter (set as default NULL), and if there are two groups, the first level of groups will set as the reference group; if there are multiple groups, it will perform an ANOVA-like testing to find markers which difference in any of the groups.

Value

a microbiomeMarker object.

Author(s)

Yang Cao

References

Robinson, Mark D., and Alicia Oshlack. "A scaling normalization method for differential expression analysis of RNA-seq data." Genome biology 11.3 (2010): 1-9.

Robinson, Mark D., Davis J. McCarthy, and Gordon K. Smyth. "edgeR: a Bioconductor package for differential expression analysis of digital gene expression data." Bioinformatics 26.1 (2010): 139-140.

See Also

edgeR::glmFit(),edgeR::glmQLFit(),edgeR::estimateDisp() ,normalize()

Examples

data(enterotypes_arumugam)
ps <- phyloseq::subset_samples(
    enterotypes_arumugam,
    Enterotype %in% c("Enterotype 3", "Enterotype 2")
)
run_edger(ps, group = "Enterotype")

HuaZou/MicrobiomeAnalysis documentation built on May 13, 2024, 11:10 a.m.