Description Usage Arguments Value Examples
View source: R/RaceID3_StemID2_class.R
This function computes a topological ordering of pseudo-temporal expression profiles of all genes by using 1-dimensional self-organizing maps.
1 |
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 |
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 |
locreg |
logical value. If |
alpha |
positive real number. This is the parameter, which controls the degree of smoothing. Larger values return smoother profiles. Default value is 0.5. |
A list of the following three components:
som |
a |
x |
pseudo-temporal expression profiles, i. e. the input expression data frame |
zs |
data frame of z-score transformed pseudo-temporal expression profiles. |
1 2 3 4 5 6 7 8 9 10 | 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)
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