get_normalized {scone} | R Documentation

## Retrieve Normalized Matrix

### Description

Given a `SconeExperiment` object created by a call to scone, it will return a matrix of normalized counts (in log scale if `log=TRUE`).

### Usage

    get_normalized(x, method, ...)

    ## S4 method for signature 'SconeExperiment,character'
    get_normalized(x, method, log = FALSE)

    ## S4 method for signature 'SconeExperiment,numeric'
    get_normalized(x, method, log = FALSE)

### 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).
`...` | additional arguments for specific methods.
`log` | logical. Should the data be returned in log-scale

### Details

If `scone` was run with `return_norm="in_memory"`, this function simply retrieves the normalized data from the `assays` slote of `object`.

If `scone` was run with `return_norm="hdf5"`, this function will read the normalized matrix from the specified hdf5 file.

If `scone` was run with `return_norm="no"`, this function will compute the normalized matrix on the fly.

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

### Value

A matrix of normalized counts in log-scale.

### Functions

- `get_normalized,SconeExperiment,character-method`: If `method` is a character, it will return the normalized 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_normalized,SconeExperiment,numeric-method`: If `method` is a numeric, it will return the normalized 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)
    res <- scone(obj, scaling=list(none=identity, uq=UQ_FN),
               evaluate=TRUE, k_ruv=0, k_qc=0,
               eval_kclust=2, bpparam = BiocParallel::SerialParam())
    top_norm = get_normalized(res,1)

[Package scone version 1.16.1 Index]