`R/generics.R`

, `R/dimensional_reduction.R`

`ScoreJackStraw.Rd`

Significant PCs should show a p-value distribution that is strongly skewed to the left compared to the null distribution. The p-value for each PC is based on a proportion test comparing the number of features with a p-value below a particular threshold (score.thresh), compared with the proportion of features expected under a uniform distribution of p-values.

ScoreJackStraw(object, ...) # S3 method for JackStrawData ScoreJackStraw(object, dims = 1:5, score.thresh = 1e-05, ...) # S3 method for DimReduc ScoreJackStraw(object, dims = 1:5, score.thresh = 1e-05, ...) # S3 method for Seurat ScoreJackStraw( object, reduction = "pca", dims = 1:5, score.thresh = 1e-05, do.plot = FALSE, ... )

object | An object |
---|---|

... | Arguments passed to other methods |

dims | Which dimensions to examine |

score.thresh | Threshold to use for the proportion test of PC significance (see Details) |

reduction | Reduction associated with JackStraw to score |

do.plot | Show plot. To return ggplot object, use |

Returns a Seurat object

Omri Wurtzel