get_design {scone} | R Documentation |
Given a SconeExperiment
object created by a call to scone, it will
return the design matrix of the selected method.
get_design(x, method) ## S4 method for signature 'SconeExperiment,character' get_design(x, method) ## S4 method for signature 'SconeExperiment,numeric' get_design(x, method)
x |
a |
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). |
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.
The design matrix.
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.
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)