importData: Import a data-frame or matrix, and associated metadata, to a...

In kevinblighe/scToolkit: scDataviz: single cell dataviz and downstream analyses

Description

Import a data-frame or matrix, and associated metadata, to a SingleCellExperiment object.

Usage

importData(
  mat,
  assayname,
  metadata = NULL,
  downsampleVar = NULL,
  verbose = TRUE
)

Arguments

mat	A data-frame or matrix of expression values. Data-frames will be coerced to matrices.
assayname	Name of the SingleCellExperiment assay slot in which data will be stored.
metadata	Metadata associated with the data contained in 'mat'. A strict rule is enforced requiring that rownames(metadata) == rownames(mat).
downsampleVar	Downsample based on variance. Removes this proportion of variables (rows) based on lesser variance. This is applied on a per sample basis. If user wishes to apply this globally on the final merged dataset, then set this to 0 and remove based on variance manually after object creation.
verbose	Boolean (TRUE / FALSE) to print messages to console or not.

Details

Import a data-frame or matrix, and associated metadata, to a SingleCellExperiment object.

Value

A SingleCellExperiment object.

Author(s)

Kevin Blighe <[e-mail]>

Examples

# create random data that follows a negative binomial
mat <- jitter(matrix(
  MASS::rnegbin(rexp(50000, rate=.1), theta = 4.5),
  ncol = 20))
colnames(mat) <- paste0('CD', 1:ncol(mat))
rownames(mat) <- paste0('cell', 1:nrow(mat))

metadata <- data.frame(
  group = rep('A', nrow(mat)),
  row.names = rownames(mat),
  stringsAsFactors = FALSE)

sce <- importData(mat,
  assayname = 'normcounts',
  metadata = metadata)

kevinblighe/scToolkit documentation built on Sept. 25, 2021, 11:29 p.m.