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.
Note
The expression-based features including:
(1) expression variance across all samples calculated with z-scores of genes under two conditions;
(2) fold change of gene expression under two conditions;
(3) expression values of genes in two conditions used for retaining the information from
actual expression values.