sconeReport: SCONE Report Browser: Browse Evaluation of Normalization...

In YosefLab/scone: Single Cell Overview of Normalized Expression data

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)

YosefLab/scone documentation built on Oct. 21, 2024, 4:39 p.m.