Description Usage Arguments Value See Also

We are often interested in finding genes that are
differentially expressed across a single-cell trajectory. Monocle3
introduces a new approach for finding such genes that draws on a powerful
technique in spatial correlation analysis, the Moran’s I test. Moran’s I is
a measure of multi-directional and multi-dimensional spatial
autocorrelation. The statistic tells you whether cells at nearby positions
on a trajectory will have similar (or dissimilar) expression levels for the
gene being tested. Although both Pearson correlation and Moran’s I ranges
from -1 to 1, the interpretation of Moran’s I is slightly different: +1
means that nearby cells will have perfectly similar expression; 0 represents
no correlation, and -1 means that neighboring cells will be
*anti-correlated*.

1 2 3 4 5 6 7 8 9 10 11 | ```
graph_test(
cds,
neighbor_graph = c("knn", "principal_graph"),
reduction_method = "UMAP",
k = 25,
method = c("Moran_I"),
alternative = "greater",
expression_family = "quasipoisson",
cores = 1,
verbose = FALSE
)
``` |

`cds` |
a cell_data_set object upon which to perform this operation |

`neighbor_graph` |
String indicating what neighbor graph to use. "principal_graph" and "knn" are supported. Default is "knn", but "principal_graph" is recommended for trajectory analysis. |

`reduction_method` |
character, the method used to reduce dimension. Currently only supported for "UMAP". |

`k` |
Number of nearest neighbors used for building the kNN graph which is passed to knn2nb function during the Moran's I (Geary's C) test procedure. |

`method` |
a character string specifying the method (currently only 'Moran_I' is supported) for detecting significant genes showing correlation along the principal graph embedded in the low dimensional space. |

`alternative` |
a character string specifying the alternative hypothesis, must be one of greater (default), less or two.sided. |

`expression_family` |
a character string specifying the expression family function used for the test. |

`cores` |
the number of cores to be used while testing each gene for differential expression. |

`verbose` |
Whether to show spatial test (Moran's I) errors and warnings. Only valid for cores = 1. |

a data frame containing the p values and q-values from the Moran's I test on the parallel arrays of models.

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