Skip to contents

Update the slots and/or meta data of the sparse eset object

updateSparseEset.Rd

This function is used to update the three slots ('assayData', 'phenoData', 'featureData') and/or 'meta data' of sparse eset object.

Usage

updateSparseEset(
  input_eset,
  dataMatrix = NULL,
  cellData = NULL,
  featureData = NULL,
  addMetaData = FALSE
)

Arguments

input_eset

The sparse eset object to update

dataMatrix

A data matrix with Features/Genes as the rows and Cells as the columns. It's row.names and colnames must be consistent with the input_eset. Default: NULL.

cellData

A data frame containing meta data of cells or NULL. It's row.names should be consistent with the colnames of input_eset. Default: NULL.

featureData

A data frame containing meata data of features or NULL. It's row.names should be consistent with the row.names of input_eset. Default: NULL.

addMetaData

Logical, whether to update the meta data of features and cells based on the expression matrix. Default: FALSE.

Value

A sparse eset object with updated information

Examples

data("pbmc14k_expression.eset")

## 1. Update the QC metrics: this will recalculate the 'nUMI', 'nFeature', 'pctMito', 'pctSpikeIn' and 'nCell'. This is very helpful when the SparseEset is subsetted or combined.
pbmc14k_raw.eset <- updateSparseEset(input_eset = pbmc14k_expression.eset, addMetaData = TRUE)
#> Updating meta data based on data matrix ...
#> Warning: The data matrix might not be a raw count matrix, since non-integer values were found. The 'nUMI' column is only valid when the values in data matrix are raw UMI counts.

## 2. Update the meta data of cells: with this, the user can add more information of cells, like clustering results, cell type.
true_label <- read.table(system.file("extdata/demo_pbmc14k/PBMC14k_trueLabel.txt.gz", package = "scMINER"), header = TRUE, row.names = 1, sep = "\t", quote = "", stringsAsFactors = FALSE)
pbmc14k_raw.eset <- updateSparseEset(input_eset = pbmc14k_expression.eset, cellData = true_label, addMetaData = TRUE)
#> The cell information of input_eset has been updated!
#> Updating meta data based on data matrix ...
#> Warning: The data matrix might not be a raw count matrix, since non-integer values were found. The 'nUMI' column is only valid when the values in data matrix are raw UMI counts.