Description Usage Arguments Value Examples

Pick the dimensionality reduction method for a dataset that gives the 2D embedding with the highest entropy

1 2 3 4 5 6 7 8 9 10 11 | ```
## S4 method for signature 'matrix'
pickDimReduction(x, flavors = c("pca", "tsne", "umap"), is.counts = TRUE)
## S4 method for signature 'SummarizedExperiment'
pickDimReduction(x)
## S4 method for signature 'Matrix'
pickDimReduction(x, flavors = c("pca", "tsne", "umap"), is.counts = TRUE)
## S4 method for signature 'DelayedMatrix'
pickDimReduction(x, flavors = c("pca", "tsne", "umap"), is.counts = TRUE)
``` |

`x` |
matrix or SummarizedExperiment object [GENES x SAMPLES] |

`flavors` |
list of dimensionality reduction algorithms to try. Currently the options are "pca", "tsne" and "umap" |

`is.counts` |
logical: is exprs count data |

name of dimensionality reduction method that gives the highest 2d entropy

1 2 | ```
x <- matrix(rnbinom(60000, size=1, prob = .1), ncol=100)
pickDimReduction(x)
``` |

BIMSBbioinfo/netSmooth documentation built on Dec. 24, 2019, 8:08 p.m.

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