truetimepattern: truetimepattern
In zji90/SEPA: SEPA

Description Usage Arguments Details Value Author(s) Examples

Identify Pattern for True Experiment Time

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

`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.

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.

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

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