prepareData: Prepare input data

In itikadi/EMOGEA: Error Modelled Gene Expression Analysis (EMOGEA) For RNA-Seq Measurements

Description

This function is meant to prepare the input to curve resolution function that calculates the profiles of a gene expression matrix measured as a function of time. The input data is an expression matrix which must have a metadata with replicate information. If there are no replicates, the total least squares implementation of the algorithm cannot be performed.

Usage

prepareData(
  expressionData,
  metaData,
  sampleColumn = "Label",
  conditionColumn = "Condition",
  genesAsRowNames = FALSE,
  applyLogTransformation = TRUE
)

Arguments

expressionData	A data.frame containing the expression data (genes as rows, samples as columns). The first column of the data.frame must contain the gene identifiers/names. Alternatively, the gene identifiers/names can be specified as row names. Duplicated or missing gene identifiers/names will be dropped.
metaData	A data.frame containing the metadata (samples as rows, information as columns). The sample names must match the ones preset in the expression data.
sampleColumn	The name of the metadata column that contains the sample names.
conditionColumn	The name of the metadata column that contains the condition names.
genesAsRowNames	Whether the genes are specified as row names or not.
applyLogTransformation	Whether to apply the log2 transformation to the expression data or not. If the data is already log transformed, the value should be FALSE.

Value

A list which contains: the processed expression data (expressionMatrix), the residual matrix (residualMatrix), the error covariance matrix (errorCovarianceMatrix).

Author(s)

Tobias K. Karakach, Federico Taverna

itikadi/EMOGEA documentation built on Dec. 20, 2021, 8:03 p.m.