logFCmatrix: Extract a matrix of log2(fold-change) values

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Extract a matrix of log2(fold-change) values

Description

Extract a matrix of log2(fold-change) values

Usage

logFCmatrix(
  edgeResult,
  featureIdentifier = "GeneSymbol",
  contrasts = NULL,
  removeNAfeatures = TRUE,
  minAveExpr = NULL
)

Arguments

edgeResult	An EdgeResult object
featureIdentifier	Character, column name in dgeTable that will be used as rownames of the result matrix
contrasts	NULL or characters; if not NULL, only logFC values of given contrasts will be returned
removeNAfeatures	Logical, if TRUE, features containing NA values are removed.
minAveExpr	NULL or numeric. If set, features with aveExpr lower than the given value is not considered. This option is helpful to remove genes that are lowly expressed which yet show strong differential expression.

Note

TODO: add edgeResult data example

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.