SEPA (version 1.2.2)

pseudotimepattern: pseudotimepattern

Description

Identify Pattern for Pseudo Temporal Cell Ordering

Usage

pseudotimepattern(expr, pseudotime, simplify = T, removeconstant = F, plot = F, gap = 10)

Arguments

expr

The matrix of gene expression profile.

pseudotime

A character data.frame or matrix of pseudo-time. First column: Cell name; Second column: pseudo-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.

plot

Whether to generate plot for genes with transition points.

gap

Number of first and last gap cells that will be excluded when considering transition points.

Value

A list. expr: original expression matrix; pseudotime: original pseudotime; pattern: a list containing results of different patterns. For single patterns, it is a named vector where values are the p-values of the t-test of the simple linear regression slope coefficient. The vector is ordered according to the p-values. For transition patterns, a data.frame containing the mean and confidence interval of the transition point. It is ordered according to the transition points; fitexpr: the fitted expression matrix

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.

Examples

data(HSMMdata)
pseudotimepattern(HSMMdata,pseudotime)