orderscore: orderscore
In TSCAN: Tools for Single-Cell Analysis

Description Usage Arguments Details Value Author(s) Examples

Calculate pseudotemporal ordering scores for orders

1	orderscore(subpopulation, orders)

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

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,...

a numeric vector of calculated POS.

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

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)