getsom: Topological ordering of pseudo-temporal expression profiles

In dynverse/StemID2: De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

Description

This function computes a topological ordering of pseudo-temporal expression profiles of all genes by using 1-dimensional self-organizing maps.

Usage

getsom(x, nb = 1000, k = 5, locreg = TRUE, alpha = 0.5)

Arguments

x	expression data frame with genes as rows and cells as columns. Gene IDs should be given as row names and cell IDs should be given as column names. The pseudo-temporal expression profile of each gene is defined by the order of cell IDs, i. e. columns, in x.
nb	positive integer number. Number of nodes of the self-organizing map. Default value is 1000.
k	positive integer number. Pseudo-temporal expression profiles are either derived using a running mean of expression values across the ordered cells with window-size k, or by a local regression (if locreg is TRUE). Default value is 5.
locreg	logical value. If TRUE, then pseudo-temporal expression profiles are derived by a local regression of expression values across the ordered cells using the function loess from the package stats. Default value is TRUE.
alpha	positive real number. This is the parameter, which controls the degree of smoothing. Larger values return smoother profiles. Default value is 0.5.

Value

A list of the following three components:

som	a som object returned by the function som of the package som
x	pseudo-temporal expression profiles, i. e. the input expression data frame x after smoothing by running mean or local regression, respectivey, and normalization. The sum of smoothened gene expression values across all cells is normalized to 1.
zs	data frame of z-score transformed pseudo-temporal expression profiles.

Examples

x <- intestine$x
y <- intestine$y
v <- intestine$v

tar <- c(6,9,13)
fb <- fateBias(x,y,tar,z=NULL,minnr=5,minnrh=10,nbfactor=5,use.dist=FALSE,seed=NULL,nbtree=NULL)
trc <- dptTraj(x,y,fb,trthr=.25,distance="euclidean",sigma=1000)
n <- trc[["t6"]]
fs  <- filterset(v,n,minexpr=2,minnumber=1)
s1d <- getsom(fs,nb=1000,k=5,locreg=TRUE,alpha=.5)

dynverse/StemID2 documentation built on May 25, 2019, 4:25 p.m.