enrichFRY: enrichFRY

In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

enrichFRY

Description

Enrichment analyzer using roast with function fry

Usage

enrichFRY(
  object,
  G,
  annot,
  sep.str = " /// ",
  symbol.col = "symbol",
  grp = NULL,
  contrast = ncol(design),
  design = NULL,
  weights = NULL,
  trend = FALSE,
  block = NULL,
  correlation = NULL,
  adjust.method = c("BH", "none"),
  min.nfeats = 3,
  max.nfeats = 1000,
  pvalueCutoff = 0.25,
  qvalueCutoff = 1
)

Arguments

object	Matrix-like data object containing log-ratios or log-expression values, with rows corresponding to features (e.g. genes) and columns to samples. Must have row names that are non-duplicated and non-empty.
G	Gene set list as returned from read_gmt.
annot	annotation for the features that has a column of the same type as in gene set list G.
sep.str	strings that separates symbols if there are multiple symbols for a feature.
symbol.col	column name or index for the symbol column in annot.
grp	Vector of sample groups. These must be valid variable names in R and the same length as ncol(object).
contrast	contrast for which the test is required. Can be an integer specifying a column of design, or the name of a column of design, or a numeric contrast vector of length equal to the number of columns of design.
design	Design matrix of the experiment, with rows corresponding to samples and columns to coefficients to be estimated.
weights	Non-negative observation weights. Can be a numeric matrix of individual weights of same size as the object, or a numeric vector of sample weights with length ncol(object), or a numeric vector of gene weights with length equal to nrow(object).
trend	Logical; should an intensity-trend be allowed for the prior variance? Default is that the prior variance is constant.
block	Vector specifying a blocking variable on the samples. Has length = ncol(object). Must be NULL if ndups > 1.
correlation	Inter-duplicate or inter-technical replicate correlation. Must be given if ndups>1 or !is.null(block).
adjust.method	Method used to adjust the p-values for multiple testing. Options,
min.nfeats	Minimum number of features (e.g. genes) needed in a gene set for testing.
max.nfeats	Maximum number of features (e.g. genes) needed in a gene set for testing.
pvalueCutoff	Cutoff value of pvalue.
qvalueCutoff	Cutoff value of qvalue.

Value

A list of 3 enrichResult instance for up-regulated, down-regulated, and mixed-regulated enriched gene sets.

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