| scTenifoldKnk {scTenifoldKnk} | R Documentation |
scTenifoldKNK
Description
Predict gene perturbations
Usage
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
)
Arguments
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. |
Author(s)
Daniel Osorio <dcosorioh@tamu.edu>
Examples
# 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)