sconeReport {scone} | R Documentation

## SCONE Report Browser: Browse Evaluation of Normalization Performance

### Description

This function opens a shiny application session for visualizing performance of a variety of normalization schemes.

### Usage

    sconeReport(
      x,
      methods,
      qc,
      bio = NULL,
      batch = NULL,
      poscon = character(),
      negcon = character(),
      eval_proj = NULL,
      eval_proj_args = NULL
    )

### Arguments

`x` | a `SconeExperiment` object
`methods` | character specifying the normalizations to report.
`qc` | matrix. QC metrics to be used for QC evaluation report. Required.
`bio` | factor. A biological condition (variation to be preserved). Default NULL.
`batch` | factor. A known batch variable (variation to be removed). Default NULL.
`poscon` | character. Genes to be used as positive controls for evaluation. These genes should be expected to change according to the biological phenomenon of interest. Default empty character.
`negcon` | character. Genes to be used as negative controls for evaluation. These genes should be expected not to change according to the biological phenomenon of interest. Default empty character.
`eval_proj` | function. Projection function for evaluation (see `score_matrix` for details). If NULL, PCA is used for projection.
`eval_proj_args` | list. List of args passed to projection function as eval_proj_args.

### Value

An object that represents the SCONE report app.

### Examples

    set.seed(101)
    mat <- matrix(rpois(1000, 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, deseq=DESEQ_FN),
               evaluate=TRUE, k_ruv=0, k_qc=0, eval_kclust=2,
               bpparam = BiocParallel::SerialParam())
    qc = as.matrix(cbind(colSums(mat),colSums(mat > 0)))
    rownames(qc) = colnames(mat)
    colnames(qc) = c("NCOUNTS","NGENES")
    ## Not run:
    sconeReport(res,rownames(get_params(res)), qc = qc)

    ## End(Not run)

[Package scone version 1.16.1 Index]