tomoSummarizedExperiment: Create an object from SummarizedExperiment

In liuwd15/tomoda: Tomo-seq data analysis

Create an object from SummarizedExperiment

Description

tomoSummarizedExperiment creates an object from a SummarizedExperiment object.

Usage

tomoSummarizedExperiment(
  se,
  min.section = 3,
  normalize = TRUE,
  normalize.method = "median",
  scale = TRUE
)

Arguments

se	A SummarizedExperiment object, it must contain at least one of 'count' assay and 'normalized' assay.
min.section	Integer. Genes expressed in less than min.section sections will be filtered out.
normalize	Logical, whether to perform normalization when creating the object. Default is TRUE.
normalize.method	Character, must be one of "median", or "cpm".
scale	Logical, whether to perform scaling when creating the object. Default is TRUE.

Value

A SummarizedExperiment object

See Also

createTomo for the generic function.

Examples

data(zh.data)
se <- SummarizedExperiment::SummarizedExperiment(assays=list(count=zh.data))
zh <- tomoSummarizedExperiment(se)

liuwd15/tomoda documentation built on March 29, 2022, 1:09 a.m.