Description Usage Arguments Value Examples

View source: R/FateID_functions.R

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

1 | ```
getsom(x, nb = 1000, alpha = 0.5)
``` |

`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. |

`alpha` |
positive real number. Pseudo-temporal expression profiles are derived by a local regression of expression values across the ordered cells using the function |

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 11 | ```
x <- intestine$x
y <- intestine$y
v <- intestine$v
tar <- c(6,9,13)
fb <- fateBias(x,y,tar,z=NULL,minnr=5,minnrh=10,nbfactor=5,use.dist=FALSE,seed=NULL,nbtree=NULL)
dr <- compdr(x,z=NULL,m="cmd",k=2,lle.n=30,tsne.perplexity=30)
pr <- prcurve(y,fb,dr,k=2,m="cmd",trthr=0.4,start=NULL)
n <- pr$trc[["t6"]]
fs <- filterset(v,n,minexpr=2,minnumber=1)
s1d <- getsom(fs,nb=1000,alpha=.5)
``` |

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