sce_extract: Extract data from a SingleCellExperiment object

In jackbibby1/SCPA: Single Cell Pathway Analysis

Extract data from a SingleCellExperiment object

Description

This function takes a SingleCellExperiment object as an input, and returns an expression matrix based on subsetting parameters. Either none, one, or two metadata features can be selected for a given input.

Usage

sce_extract(
  sce_object,
  assay_name = "logcounts",
  meta1 = NULL,
  value_meta1 = NULL,
  meta2 = NULL,
  value_meta2 = NULL,
  pseudocount = 0.001
)

Arguments

sce_object	SingleCellExperiment object containing expression data
assay_name	Name of assay to pull from. Defaults to "logcounts"
meta1	Metadata column to subset
value_meta1	Value to select within meta1 column
meta2	Metadata column to subset
value_meta2	Value to select within meta2 column
pseudocount	Pseudocount to add to data. Defaults to 0.001

Value

Matrix containing count values of selected populations

Examples

## Not run: 
cd4 <- sce_extract(
   sce_object,
   meta1 = "Hour",
   value_meta1 = 12,
   meta2 = "Cell_Type",
   value_meta2 = "CD4"
)

## End(Not run)

jackbibby1/SCPA documentation built on May 14, 2024, 7:16 a.m.