findMarkers {celda} | R Documentation

## Generate decision tree from single-cell clustering output.

### Description

Uses decision tree procudure to generate a set of rules for each cell cluster defined by a single-cell clustering. Splits are determined by one of two metrics at each split: a one-off metric to determine rules for identifying clusters by a single feature, and a balanced metric to determine rules for identifying sets of similar clusters.

### Usage

    findMarkers(
      features,
      class,
      cellTypes,
      oneoffMetric = c("modified F1", "pairwise AUC"),
      threshold = 0.95,
      reuseFeatures = FALSE,
      altSplit = TRUE,
      consecutiveOneoff = TRUE
    )

### Arguments

`features` | A L(features) by N(samples) numeric matrix.
`class` | A vector of K label assignemnts.
`cellTypes` | List where each element is a cell type and all the clusters within that cell type (i.e. subtypes).
`oneoffMetric` | A character string. What one-off metric to run, either 'modified F1' or 'pairwise AUC'.
`threshold` | A numeric value. The threshold for the oneoff metric to use between 0 and 1, 0.95 by default. Smaller values will result is more one-off splits.
`reuseFeatures` | Logical. Whether or not a feature can be used more than once on the same cluster. Default is TRUE.
`altSplit` | Logical. Whether or not to force a marker for clusters that are solely defined by the absence of markers. Defulault is TRUE
`consecutiveOneoff` | Logical. Whether or not to allow one-off splits at consecutive brances. Default it TRUE

### Value

A named list with five elements.

- rules - A named list with one 'data.frame' for every label. Each 'data.frame' has five columns and gives the set of rules for disinguishing each label.

  - feature - Feature identifier.

  - direction - Relationship to feature value, -1 if less than, 1 if greater than.

  - value - The feature value which defines the decision boundary

  - stat - The performance value returned by the splitting metric for this split.

  - statUsed - Which performance metric was used. "IG" if information gain and "OO" if one-off.

  - level - The level of the tree at which is rule was defined. 1 is the level of the first split of the tree.

- dendro - A dendrogram object of the decision tree output

- summaryMatrix - A K(labels) by L(features) matrix representation of the decision rules. Columns denote features and rows denote labels. Non-0 values denote instances where a feature was used on a given label. Positive and negative values denote whether the values of the label for that feature were greater than or less than the decision threshold, respectively. The magnitude of Non-0 values denote the level at which the feature was used, where the first split has a magnitude of 1. Note, if reuse_features = TRUE, only the final usage of a feature for a given label is shown.

- prediction - A character vector of label of predictions of the training data using the final model. "MISSING" if label prediction was ambiguous.

- performance - A named list denoting the training performance of the model.

  - accuracy - (number correct/number of samples) for the whole set of samples.

  - balAcc - mean sensitivity across all labels

  - meanPrecision - mean precision across all labels

  - correct - the number of correct predictions of each label

  - sizes - the number of actual counts of each label

  - sensitivity - the sensitivity of the prediciton of each label.

  - precision - the precision of the prediciton of each label.

### Examples

    library(M3DExampleData)
    counts <- M3DExampleData::Mmus_example_list$data
    # subset 100 genes for fast clustering
    counts <- as.matrix(counts[1500:2000, ])
    # cluster genes into 10 modules for quick demo
    cm <- celda_CG(counts = counts, L = 10, K = 5, verbose = FALSE)
    # Get features matrix and cluster assignments
    factorized <- factorizeMatrix(counts, cm)
    features <- factorized$proportions$cell
    class <- clusters(cm)$z
    # Generate Decision Tree
    DecTree <- findMarkers(features,
                               class,
                               oneoffMetric = "modified F1",
                               threshold = 1,
                               consecutiveOneoff = FALSE)

    # Plot dendrogram
    plotDendro(DecTree)

[Package celda version 1.2.4 Index]