edger_contrasts: Apply edgeR's glmQLFit or glmFit, glmQLFTest, glmLRT, or...

In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

Apply edgeR's glmQLFit or glmFit, glmQLFTest, glmLRT, or glmWeightedF to one or more contrasts, and return a list

Description

Apply edgeR's glmQLFit, or glmFit, glmQLFTest, glmLRT, or glmWeightedF to one or more contrasts, and return a list

Usage

edger_contrasts(
  dge,
  grp = NULL,
  contrast.v,
  add.means = !is.null(grp),
  design = NULL,
  cols = c("PValue", "FDR", "logFC"),
  test = "QLFT",
  plot = FALSE
)

Arguments

dge	DGEList object.
grp	Vector of sample groups. These must be valid variable names in R and the same length as ncol(object).
contrast.v	Named vector of contrasts, passed to makeContrasts.
add.means	Logical indicating if (unweighted) group means per row should be added to the output.
design	Design matrix of the experiment, with rows corresponding to samples and columns to coefficients to be estimated.
cols	Columns of topTable output to include. Possibilities include "logFC", "AveExpr", "z", "t", "P.Value", "adj.P.Val", "B". Some of these column names are then changed here. If logFC is specified, FC will automatically also be given.
test	QLFT, LRT or WeightedFT.
plot	Logical indicate if to plot the QC metrics.

Details

If design is NULL and grp is given, design will be calculated as model.matrix(~0+grp). However, grp isn't needed if design is provided & add.means is FALSE.

jdreyf/jdcbioinfo documentation built on April 15, 2024, 6:37 p.m.