Description Usage Arguments Value Author(s) References Examples

View source: R/choosing_number_of_types.R

chty is used to get number of types for the data.

1 |

`data` |
an optional n by p count data matrix. The p columns of the matrix are different variables and the n rows are samples. Each column should contain at lest one none zero entry. When n = 1, it is a row vector. |

`y` |
a binary variable contains classification information of the data. Usually one group is labelled as "0" and the other as "1". |

`k` |
a value gives the number of folds used in cross validation when choosing number of types. |

`maxr` |
a number gives the upper bound of the number of types. |

`r1 ` |
the suggested number of types for class labeled as 1. |

`r2 ` |
the suggested number of types for class labeled as 0. |

Yun Cai, Hong Gu and Toby Kenney

Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
##we use the simulated data spdata here
##the spdata is simulated from feature matrix combined by 2
#3types features from one group and 3 types from the other.
##choose number of types using our function
##2-folds cross validation is used here
##the upper bound of number of types for both classes is 2
##remove all zero variables from the data
spdata.rm=spdata[c(1:4,41:44),colSums(spdata)!=0]
y=c(rep(1,4),rep(0,4))
types=chty(spdata.rm,y,2,2)
#number of types for class labeled as 1
nmb1 = types$r1
#number of types for class labeled as 0
nmb2 = types$r2
``` |

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