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**monocle**: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq**residualMatrix**: Response values

# Response values

### Description

Generates a matrix of response values for a set of fitted models

### Usage

1 | ```
residualMatrix(models, residual_type = "response", cores = 1)
``` |

### Arguments

`models` |
a list of models, e.g. as returned by fitModels() |

`residual_type` |
the response desired, as accepted by VGAM's predict function |

`cores` |
number of cores used for calculation |

### Value

a matrix where each row is a vector of response values for a particular feature's model, and columns are cells.

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- BEAM: Branched expression analysis modeling (BEAM)
- branchTest: Test for branch-dependent expression
- buildBranchCellDataSet: Build a CellDataSet that splits cells among two branches
- calABCs: Compute the area between curves (ABC) for branch-dependent...
- calibrate_per_cell_total_proposal: Calibrate_per_cell_total_proposal
- calILRs: Calculate the Instantaneous Log Ratio between two branches
- CellDataSet: The CellDataSet class
- CellDataSet-methods: Methods for the CellDataSet class
- cellPairwiseDistances: Get the matrix of pairwise distances between cells
- cellPairwiseDistances-set: Sets the matrix containing distances between each pair of...
- CellType: The CellType class
- CellTypeHierarchy: The CellTypeHierarchy class
- clusterCells: Cluster cells into a specified number of groups.
- clusterGenes: Clusters genes by pseudotime trend.
- compareModels: Compare model fits
- detectBifurcationPoint: Calculate divergence times for branch-dependent genes
- detectGenes: Sets the global expression detection threshold to be used...
- differentialGeneTest: Test genes for differential expression
- diff_test_helper: Helper function for parallel differential expression testing
- dispersionTable: Retrieve a table of values specifying the mean-variance...
- estimateDispersionsForCellDataSet: Helper function to estimate dispersions
- estimateSizeFactorsForMatrix: Function to calculate the size factor for the single-cell...
- estimate_t: Find the most commonly occuring relative expression value in...
- extract_good_branched_ordering: Extract a linear ordering of cells from a PQ tree
- fitModel: Fits a model for each gene in a CellDataSet object.
- fit_model_helper: Helper function for parallel VGAM fitting
- genSmoothCurveResiduals: Fit smooth spline curves and return the residuals matrix
- genSmoothCurves: Fit smooth spline curves and return the response matrix
- get_classic_muscle_markers: Return the names of classic muscle genes
- load_HSMM: Build a CellDataSet from the HSMMSingleCell package
- load_HSMM_markers: Return a CellDataSet of classic muscle genes
- load_lung: Build a CellDataSet from the data stored in inst/extdata...
- markerDiffTable: Test genes for cell type-dependent expression
- mcesApply: Multicore apply-like function for CellDataSet
- minSpanningTree: Retrieves the minimum spanning tree generated by Monocle...
- minSpanningTree-set: Set the minimum spanning tree generated by Monocle during...
- newCellDataSet: Creates a new CellDateSet object.
- newCellTypeHierarchy: Classify cells according to a set of markers
- orderCells: Orders cells according to pseudotime.
- order_p_node: Return an ordering for a P node in the PQ tree
- package-deprecated: Plots the minimum spanning tree on cells. This function is...
- plot_cell_trajectory: Plots the minimum spanning tree on cells.
- plot_clusters: Plots kinetic clusters of genes.
- plot_coexpression_matrix: Not sure we're ready to release this one quite yet: Plot the...
- plot_genes_branched_heatmap: Create a heatmap to demonstrate the bifurcation of gene...
- plot_genes_branched_pseudotime: Plot the branch genes in pseduotime with separate branch...
- plot_genes_in_pseudotime: Plots expression for one or more genes as a function of...
- plot_genes_jitter: Plots expression for one or more genes as a jittered, grouped...
- plot_genes_positive_cells: Plots the number of cells expressing one or more genes as a...
- plot_ordering_genes: Plots genes by mean vs. dispersion, highlighting those...
- plot_pseudotime_heatmap: Plots a pseudotime-ordered, row-centered heatmap
- pq_helper: Recursively builds and returns a PQ tree for the MST
- reducedDimA: Get the weights needed to lift cells back to high dimensional...
- reducedDimA-set: Get the weights needed to lift cells back to high dimensional...
- reducedDimK: Retrieves the the whitening matrix during independent...
- reducedDimK-set: Sets the the whitening matrix during independent component...
- reducedDimS: Retrieves the coordinates of each cell in the...
- reducedDimS-set: Set embedding coordinates of each cell in a CellDataSet.
- reducedDimW: Get the whitened expression values for a CellDataSet.
- reducedDimW-set: Sets the whitened expression values for each cell prior to...
- reduceDimension: Compute a projection of a CellDataSet object into a lower...
- relative2abs: Transform relative expression values into absolute transcript...
- residualMatrix: Response values
- responseMatrix: Response values
- scale_pseudotime: Scale pseudotime to be in the range from 0 to 100
- selectNegentropyGenes: Filter genes with extremely high or low negentropy
- selectTopMarkers: Select the most cell type specific markers
- setOrderingFilter: Sets the features (e.g. genes) to be used for ordering cells...
- spike_df: Spike-in transcripts data.
- vstExprs: Return a variance-stabilized matrix of expression values