mlDNA (version 1.1)

expFeatureMatrix: Expression-based feature matrix

Description

This function generates expression-based features for each gene with the consideration of z-scores, fold changes and actural expression values.

Usage

expFeatureMatrix(expMat1, sampleVec1, expMat2, sampleVec2,  logTransformed = TRUE, base = 2,  features = c("zscore", "foldchange", "cv", "expression"))

Arguments

expMat1

a numeric matrix recording gene expression data from condition 1. Each row represent the expression values of one gene, each column represents the expression values of all genes from one biological experiment.

sampleVec1

a numeric vector representing biological replication (or different time points) and technical replication for condition 1. For instance, c(1,1,2,2,3,3) denotes three biological replications, and two technicial replications for each biological sample.

expMat2

a numeric matrix recording gene expression data from condition 2.

sampleVec2

a numeric vector representing biological experiments and technical replications for condition 2. Definition is similar as sampleVec1.

logTransformed

logic value, TRUE indicates that the expression data in expMat1 and expMat2 have been log-transformed.

base

base of log transformation.

features

A character fector specifying different features will be used to generate feature matrix.

Value

value

a numeric matrix with express-based features for each gene.

Examples

 ## Not run: 
#  
#    ##generated expression features
#    sampleVec1 <- c(1, 2, 3, 4, 5, 6)
#    sampleVec2 <- c(1, 2, 3, 4, 5, 6)
#    featureMat <- expFeatureMatrix( expMat1 = ControlExpMat, sampleVec1 = sampleVec1, 
#                                    expMat2 = SaltExpMat, sampleVec2 = sampleVec2, 
#                                    logTransformed = TRUE, base = 2, 
#                                features = c("zscore", "foldchange", "cv", "expression"))
# ## End(Not run)