get_design {scone} | R Documentation

## Retrieve Design Matrix

### Description

Given a `SconeExperiment` object created by a call to scone, it will return the design matrix of the selected method.

### Usage

    get_design(x, method)

    ## S4 method for signature 'SconeExperiment,character'
    get_design(x, method)

    ## S4 method for signature 'SconeExperiment,numeric'
    get_design(x, method)

### Arguments

`x` | a `SconeExperiment` object containing the results of `scone`.
`method` | character or numeric. Either a string identifying the normalization scheme to be retrieved, or a numeric index with the rank of the normalization method to retrieve (according to scone ranking of normalizations).

### Details

The numeric method will always return the design matrix corresponding to row `method` of the `scone_params` slot. This means that if `scone` was run with `eval=TRUE`, `get_design(x, 1)` will return the top ranked method. If `scone` was run with `eval=FALSE`, `get_design(x, 1)` will return the first normalization in the order saved by scone.

### Value

The design matrix.

### Functions

- `get_design,SconeExperiment,character-method`: If `method` is a character, it will return the design matrix corresponding to the normalization scheme specified by the character string. The string must be one of the `row.names` of the slot `scone_params`.

- `get_design,SconeExperiment,numeric-method`: If `method` is a numeric, it will return the design matrix according to the scone ranking.

### Examples

    set.seed(42)
    mat <- matrix(rpois(500, lambda = 5), ncol=10)
    colnames(mat) <- paste("X", 1:ncol(mat), sep="")
    obj <- SconeExperiment(mat, bio = factor(rep(c(1,2),each = 5)),
               batch = factor(rep(c(1,2),times = 5)))
    res <- scone(obj, scaling=list(none=identity, uq=UQ_FN),
               evaluate=TRUE, k_ruv=0, k_qc=0,
               adjust_batch = "yes", adjust_bio = "yes",
               eval_kclust=2, bpparam = BiocParallel::SerialParam())
    design_top = get_design(res,1)

[Package scone version 1.16.1 Index]