tomoMatrix: Create an object from matrix

In tomoda: Tomo-seq data analysis

Description

tomoMatrix creates an object from raw read count matrix or normalized read count matrix.

Usage

tomoMatrix(
  matrix.count = NULL,
  matrix.normalized = NULL,
  min.section = 3,
  normalize = TRUE,
  normalize.method = "median",
  scale = TRUE
)

Arguments

matrix.count	A numeric matrix or matrix-like data stucture that can be coverted to matrix, with genes with rows, sections as columns and values as raw read counts. Columns should be sorted according to section numbers.
matrix.normalized	A numeric matrix or matrix-like data stucture that can be coverted to matrix, with genes as rows, sections as columns and values as normalized read counts. Columns should be sorted according to order of sections.
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)
zh <- tomoMatrix(zh.data)

tomoda documentation built on Nov. 8, 2020, 8:10 p.m.