R implementation of the LEfSe method 2 — lefser2 • MicrobiomeBenchmarkDataAnalyses

lefser2 is an adaptation from the lefser function. This adaptation allows the inclusion of the raw p-values of the KW test on the output.

lefser2(
  expr,
  kruskal.threshold = 0.05,
  wilcox.threshold = 0.05,
  lda.threshold = 2,
  groupCol = "GROUP",
  blockCol = NULL,
  assay = 1L,
  trim.names = FALSE,
  log = FALSE
)

Arguments

expr: A SummarizedExperiment with expression data.
kruskal.threshold: numeric(1) The p-value for the Kruskal-Wallis Rank Sum Test (default 0.05).
wilcox.threshold: numeric(1) The p-value for the Wilcoxon Rank-Sum Test when 'blockCol' is present (default 0.05).
lda.threshold: numeric(1) The effect size threshold (default 2.0).
groupCol: character(1) Column name in colData(expr) indicating groups, usually a factor with two levels (e.g., c("cases", "controls"); default "GROUP").
blockCol: character(1) Optional column name in colData(expr) indicating the blocks, usually a factor with two levels (e.g., c("adult", "senior"); default NULL).
assay: The i-th assay matrix in the SummarizedExperiment ('expr'; default 1).
trim.names: If TRUE extracts the most specific taxonomic rank of organism.
log: If TRUE, matrix is exponentiated (exp). Default is FALSE.

Value

The function returns a data frame with three columns, which are names of microorganisms, their LDA scores, and kruskal wallis p-values.