importanceADT {CiteFuse} | R Documentation

## importanceADT

### Description

A function to calculate the importance score of ADT

### Usage

    importanceADT(
      sce,
      altExp_name = "ADT",
      exprs_value = "logcounts",
      method = c("randomForest", "PCA"),
      group = NULL,
      subsample = TRUE,
      times = 10,
      prop = 0.8,
      k_pca = 5,
      remove_first_PC = TRUE,
      ...
    )

### Arguments

`sce` | A singlecellexperiment object
`altExp_name` | A character indicates which expression matrix is used. by default is none (i.e. RNA).
`exprs_value` | A character indicates which expression value in assayNames is used.
`method` | A character indicates the method of ADT importance calculation, either randomForest or PCA
`group` | A vector indicates the grouping of the data (for random forest)
`subsample` | Whether perform subsampling (for random forest)
`times` | A numeric indicates the times of subsampling is performed (for random forest)
`prop` | A numeric indicates the proportion of cells are subsampled from the whole data (for random forest)
`k_pca` | Number of principal component will be used to calculate the loading scores (for PCA)
`remove_first_PC` | A logical input indicates whether the first component will be removed from calculation (for PCA).
`...` | other arguments to 'randomForest()' or 'prcomp()' function

### Details

For random forest, the importance scores are based on features importance. For PCA, it implements the method proposed in Levin et al (based on the loading of features).

### Value

A SingleCellExperiment object

### References

Levine, J.H., Simonds, E.F., Bendall, S.C., Davis, K.L., El-ad, D.A., Tadmor, M.D., Litvin, O., Fienberg, H.G., Jager, A., Zunder, E.R. and Finck, R., 2015. Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Cell, 162(1), pp.184-197.

### Examples

    data("sce_control_subset", package = "CiteFuse")
    sce_control_subset <- importanceADT(sce_control_subset,
    group = sce_control_subset$SNF_W_louvain,
    subsample = TRUE)

[Package CiteFuse version 1.2.1 Index]