tfPS: Transform Phylostratum Values

In drostlab/myTAI: Evolutionary Transcriptomics

Transform Phylostratum Values

Description

This function performs transformation of phylostratum values.

Usage

tfPS(ExpressionSet, transform)

Arguments

ExpressionSet	a standard PhyloExpressionSet object.
transform	a character vector of any valid function that transforms PS values. Possible values can be: transform = "qr" (or "quantilerank") : quantile rank transformation analogous to Julia function StatsBase.quantilerank using method = :tied.

Details

This function transforms the phylostratum assignment. The return value of this function is a PhyloExpressionSet object with transformed phylostratum tfPhylostratum as the first column, satisfying is.ExpressionSet. Note that the input transform must be an available function, currently limited to only "qr" (or "quantilerank").

Value

a standard PhloExpressionSet object storing transformed Phylostratum levels.

Author(s)

Jaruwatana Sodai Lotharukpong and Lukas Maischak

See Also

tf

Examples

# source the example dataset
data(PhyloExpressionSetExample)
 
# get the relative expression profiles for each phylostratum
tfPES <- tfPS(PhyloExpressionSetExample, transform = "qr")
head(tfPES)

drostlab/myTAI documentation built on June 13, 2025, 6:24 a.m.