truetimepattern

Description

Identify Pattern for True Experiment Time

Usage

1
truetimepattern(expr, truetime, simplify = T, removeconstant = F)

Arguments

expr

The matrix of gene expression profile.

truetime

A character data.frame or matrix of true experimental time. First column: Cell name; Second column: experiment time.

simplify

Whether to simplify pattern so that same neiboring patterns will be reduced to one. For example "up_up_constant" will be simplied to "up_constant".

removeconstant

Whether to remove all constant patterns. For example "up_up_constant" will be simplied to "up_up". This step will be performed before simplify.

Details

Identify the gene expression patterns for true experiment time. For the expressions of each gene, the function performs t-tests for cells from neighboring time points. The expression pattern for cells from neiboring time points could be increasing, decreasing or constant. All patterns are concatenated using "-" to form the final pattern.

Value

A named vector or patterns. The names corresponds to gene names.

Author(s)

Zhicheng Ji, Hongkai Ji <zji4@zji4.edu>

Examples

1
2