Description Usage Arguments Author(s) Examples

View source: R/scTenifoldKnk.R

Predict gene perturbations

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
scTenifoldKnk(
countMatrix,
gKO = NULL,
qc_mtThreshold = 0.1,
qc_minLSize = 1000,
nc_lambda = 0,
nc_nNet = 10,
nc_nCells = 500,
nc_nComp = 3,
nc_scaleScores = TRUE,
nc_symmetric = FALSE,
nc_q = 0.9,
td_K = 3,
td_maxIter = 1000,
td_maxError = 1e-05,
td_nDecimal = 3,
ma_nDim = 2
)
``` |

`countMatrix` |
countMatrix |

`gKO` |
gKO |

`qc_mtThreshold` |
A decimal value between 0 and 1. Defines the maximum ratio of mitochondrial reads (mithocondrial reads / library size) present in a cell to be included in the analysis. It's computed using the symbol genes starting with 'MT-' non-case sensitive. |

`qc_minLSize` |
An integer value. Defines the minimum library size required for a cell to be included in the analysis. |

`nc_lambda` |
A continuous value between 0 and 1. Defines the multiplicative value (1-lambda) to be applied over the weaker edge connecting two genes to maximize the adjacency matrix directionality. |

`nc_nNet` |
An integer value. The number of networks based on principal components regression to generate. |

`nc_nCells` |
An integer value. The number of cells to subsample each time to generate a network. |

`nc_nComp` |
An integer value. The number of principal components in PCA to generate the networks. Should be greater than 2 and lower than the total number of genes. |

`nc_scaleScores` |
A boolean value (TRUE/FALSE), if TRUE, the weights will be normalized such that the maximum absolute value is 1. |

`nc_symmetric` |
A boolean value (TRUE/FALSE), if TRUE, the weights matrix returned will be symmetric. |

`nc_q` |
A decimal value between 0 and 1. Defines the cut-off threshold of top q% relationships to be returned. |

`td_K` |
An integer value. Defines the number of rank-one tensors used to approximate the data using CANDECOMP/PARAFAC (CP) Tensor Decomposition. |

`td_maxIter` |
An integer value. Defines the maximum number of iterations if error stay above |

`td_maxError` |
A decimal value between 0 and 1. Defines the relative Frobenius norm error tolerance. |

`td_nDecimal` |
An integer value indicating the number of decimal places to be used. |

`ma_nDim` |
An integer value. Defines the number of dimensions of the low-dimensional feature space to be returned from the non-linear manifold alignment. |

Daniel Osorio <dcosorioh@tamu.edu>

1 2 3 4 5 6 | ```
# Loading single-cell data
scRNAseq <- system.file("single-cell/example.csv",package="scTenifoldKnk")
scRNAseq <- read.csv(scRNAseq, row.names = 1)
# Running scTenifoldKnk
scTenifoldKnk(countMatrix = scRNAseq, gKO = 'G100', qc_minLSize = 0)
``` |

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