truetimepattern: truetimepattern

In SEPA: SEPA

Description

Identify Pattern for True Experiment Time

Usage

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 <[e-mail]>

Examples

data(HSMMdata)
truetimepattern(HSMMdata,truetime)

SEPA documentation built on May 6, 2019, 2:42 a.m.