orderscore {TSCAN} | R Documentation

## orderscore

### Description

Calculate pseudotemporal ordering scores for orders

### Usage

    orderscore(subpopulation, orders)

### Arguments

`subpopulation` | Data frame with two columns. First column: cell names. Second column: sub-population codes.
`orders` | A list with various length containing pseudotime orderings.

### Details

This function calculates pseudotemporal ordering scores (POS) based on the sub-population information and order information given by users. Cells should come from at least two cell sub-populations. These sub-population should be coded as 0,1,2,...

### Value

a numeric vector of calculated POS.

### Author(s)

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

### Examples

    data(lpsdata)
    procdata <- preprocess(lpsdata)
    subpopulation <- data.frame(cell = colnames(procdata), sub = ifelse(grepl("Unstimulated",colnames(procdata)),0,1), stringsAsFactors = FALSE)
    lpsmclust <- exprmclust(procdata)
    #Comparing default TSCAN ordering and tuned TSCAN ordering
    order1 <- TSCANorder(lpsmclust)
    order2 <- TSCANorder(lpsmclust, c(1,2,3))
    orders <- list(order1,order2)
    orderscore(subpopulation, orders)

[Package TSCAN version 1.20.0 Index]