get_design: Retrieve Design Matrix

In scone: Single Cell Overview of Normalized Expression data

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.

Methods (by class)

• x = SconeExperiment,method = character: 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.

• x = SconeExperiment,method = numeric: 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)

scone documentation built on Nov. 8, 2020, 5:20 p.m.