CollapseReplicates: Combine Replicates in an ExpressionSet

In myTAI: Evolutionary Transcriptomics

Description

This function takes an ExpressionSet object storing either a constant or variable number of biological or technical replicates per stage and collapses replicate expression levels using a defined FUN (window function).

Usage

CollapseReplicates(ExpressionSet, nrep, FUN, stage.names = NULL)

Arguments

ExpressionSet	a standard PhyloExpressionSet or DivergenceExpressionSet object.
nrep	either a numeric value specifying the constant number of replicates per stage or a numeric vector specifying the variable number of replicates for each stage position.
FUN	a window function (e.g., mean, median, max, min, etc.) specifying how replicate expression levels should be collapsed.
stage.names	a character vector specifying the new names of collapsed stages.

Author(s)

Hajk-Georg Drost

Examples

data(PhyloExpressionSetExample)

# combine the expression levels of the 2 replicates (const) per stage
# using mean as window function and rename new stages: "S1","S2","S3"
CollapseReplicates(ExpressionSet = PhyloExpressionSetExample[1:5,1:8], 
                   nrep          = 2, 
                   FUN           = mean, 
                   stage.names   = c("S1","S2","S3"))

# combine the expression levels of the 2 replicates (stage one), 2 replicates (stage two),
# and 3 replicates (stage three) using mean as window function 
# and rename new stages: "S1","S2","S3"
CollapseReplicates(ExpressionSet = PhyloExpressionSetExample[1:5,1:9], 
                   nrep          = c(2,2,3), 
                   FUN           = mean, 
                   stage.names   = c("S1","S2","S3"))

myTAI documentation built on Feb. 24, 2021, 9:06 a.m.