EMSet: EMSet

In IMB-Computational-Genomics-Lab/ascend: ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

Description

EMSet generates a EMSet object for use with the 'ascend' package. This object contains an expression matrix, associated metadata, downstream analysis and a log documenting the actions used to shape the data in this object.

Usage

## S4 method for signature 'EMSet'
show(object)

EMSet(x, colInfo = NULL, colData = NULL, rowInfo = NULL,
  rowData = NULL, controls = NULL)

Arguments

object	EMSet
x	An object containing count data. The counts can be stored in the following formats: SingleCellExperiment, "counts" in a list or SimpleList, dense matrix or sparse matrix.
colInfo	A data frame containing cell-related metadata.
colData	A data frame containing cell-related data.
rowInfo	A data frame containing gene-related metadata.
rowData	A data frame containing gene-related data.
controls	A named list containing control genes grouped into named control groups.

Value

An EMSet object.

Examples

# Randomly generate count matrix
count_matrix <- matrix(sample(0:1, 100, replace=TRUE),10,10)

# Generate cell barcodes
cell_barcodes <- paste0("Cell-", 1:10)
gene_ids <- paste0("Gene-", 1:10)

# Add to matrix
colnames(count_matrix) <- cell_barcodes
rownames(count_matrix) <- gene_ids

# Create an EMSet
# EMSet from a list
em_set <- EMSet(list(counts = count_matrix))

# EMSet from a matrix
em_set <- EMSet(count_matrix)

IMB-Computational-Genomics-Lab/ascend documentation built on Aug. 29, 2019, 4:10 a.m.