differentialExpression: Differential expression

In VEuPathDB/veupathUtils: General Helper Functions for VEuPathDB Projects

Differential expression

Description

This function returns the fold change and associated p value for a differential expression analysis comparing samples in two groups.

Usage

differentialExpression(
  collection,
  comparator,
  method = c("DESeq"),
  pValueFloor = P_VALUE_FLOOR,
  verbose = c(TRUE, FALSE)
)

Arguments

collection	CollectionWithMetadata object
comparator	Comparator object specifying the variable and values or bins to be used in dividing samples into groups.
method	string defining the the differential abundance method. Accepted values are 'DESeq2' and 'Maaslin2'.
pValueFloor	numeric value that indicates the smallest p value that should be returned. The corresponding adjusted p value floor will also be updated based on this value, and will be set to the maximum adjusted p value of all floored p values. The default value uses the P_VALUE_FLOOR=1e-200 constant defined in this package.
verbose	boolean indicating if timed logging is desired

Value

ComputeResult object

VEuPathDB/veupathUtils documentation built on Feb. 8, 2025, 12:29 p.m.