get_edgeR_results: User friendly interface to edgeR for microbiome data

In waldronlab/nychanesmicrobiome: Analysis of the NYC-HANES Microbiome Specimens

User friendly interface to edgeR for microbiome data

Description

Returns an object of class topTags containing results filtered by FDR < alpha for one comparison. get_edgeR_results_all_levels() returns a list of topTags objects returned by get_edgeR_results() for all levels of the first variable in the formula.

Usage

get_edgeR_results(
  formla,
  pseq = NYC_HANES,
  method = c("BH", "IHW"),
  coef = 2,
  alph = 0.01,
  filtering = method[1] == "BH",
  countMinimum = 8,
  percentMinimumHaveCount = NULL,
  nMinimumHaveCount = 3,
  NA.RM = TRUE
)

get_edger_results_all_levels(formla, ...)

edger_list_to_data.frame(list_models)

get_all_edgeR_models(
  vars,
  varlabels = vars,
  adjusted_for,
  to.data.frame = TRUE,
  ...
)

Arguments

formla	formula. specifies the design matrix used by edgeR::glmFit.
pseq	object of class phyloseq
method	character. Specifies the method of multiple testing correction to apply, either "BH" (Benjamini-Hochberg) or "IHW" (independent hypothesis weighting).
coef	integer. Specifies which linear model coefficient to test (default 2).
alph	numeric. Specifies what FDR level is considered alpha, and only keeps results with FDR less than this number.
filtering	logical. Whether or not to apply pre-filtering.
countMinimum	integer. If filtering==TRUE, the minimum count required for an OTU to be retained. Requires either percentMinimumHaveCount or nMinimumHaveCount.
percentMinimumHaveCount	numeric. If filtering==TRUE, the minimum percentage of samples that must have countMinimum counts for an OTU to be retained.
nMinimumHaveCount	numeric. If filtering==TRUE, the minimum number of samples that must have countMinimum counts for an OTU to be retained.
NA.RM	logical. Whether or not to remove samples with NA values in the sample_data().
...	further arguments passed to get_edgeR_results
vars	character vector, containing names of each independent variable for which you would like a separate model.
varlabels	character vector, containing variable labels for printing
adjusted_for	character vector, containing names of the additional adjustment variables to include in each model
to.data.frame	logical. Whether or not to return a combined data.frame of all model results, rather than the default list.

waldronlab/nychanesmicrobiome documentation built on April 21, 2024, 8:52 a.m.