FoldChange: Fold Change

In satijalab/seurat: Tools for Single Cell Genomics

Fold Change

Description

Calculate log fold change and percentage of cells expressing each feature for different identity classes.

Usage

FoldChange(object, ...)

## Default S3 method:
FoldChange(object, cells.1, cells.2, mean.fxn, fc.name, features = NULL, ...)

## S3 method for class 'Assay'
FoldChange(
  object,
  cells.1,
  cells.2,
  features = NULL,
  slot = "data",
  pseudocount.use = 1,
  fc.name = NULL,
  mean.fxn = NULL,
  base = 2,
  norm.method = NULL,
  ...
)

## S3 method for class 'SCTAssay'
FoldChange(
  object,
  cells.1,
  cells.2,
  features = NULL,
  slot = "data",
  pseudocount.use = 1,
  fc.name = NULL,
  mean.fxn = NULL,
  base = 2,
  ...
)

## S3 method for class 'DimReduc'
FoldChange(
  object,
  cells.1,
  cells.2,
  features = NULL,
  slot = NULL,
  pseudocount.use = 1,
  fc.name = NULL,
  mean.fxn = NULL,
  ...
)

## S3 method for class 'Seurat'
FoldChange(
  object,
  ident.1 = NULL,
  ident.2 = NULL,
  group.by = NULL,
  subset.ident = NULL,
  assay = NULL,
  slot = "data",
  reduction = NULL,
  features = NULL,
  pseudocount.use = 1,
  mean.fxn = NULL,
  base = 2,
  fc.name = NULL,
  ...
)

Arguments

object	A Seurat object
...	Arguments passed to other methods
cells.1	Vector of cell names belonging to group 1
cells.2	Vector of cell names belonging to group 2
mean.fxn	Function to use for fold change or average difference calculation
fc.name	Name of the fold change, average difference, or custom function column in the output data.frame
features	Features to calculate fold change for. If NULL, use all features
slot	Slot to pull data from
pseudocount.use	Pseudocount to add to averaged expression values when calculating logFC.
base	The base with respect to which logarithms are computed.
norm.method	Normalization method for mean function selection when slot is “data”
ident.1	Identity class to calculate fold change for; pass an object of class phylo or 'clustertree' to calculate fold change for a node in a cluster tree; passing 'clustertree' requires BuildClusterTree to have been run
ident.2	A second identity class for comparison; if NULL, use all other cells for comparison; if an object of class phylo or 'clustertree' is passed to ident.1, must pass a node to calculate fold change for
group.by	Regroup cells into a different identity class prior to calculating fold change (see example in FindMarkers)
subset.ident	Subset a particular identity class prior to regrouping. Only relevant if group.by is set (see example in FindMarkers)
assay	Assay to use in fold change calculation
reduction	Reduction to use - will calculate average difference on cell embeddings

Details

If the slot is scale.data or a reduction is specified, average difference is returned instead of log fold change and the column is named "avg_diff". Otherwise, log2 fold change is returned with column named "avg_log2_FC".

Value

Returns a data.frame

See Also

FindMarkers

Examples

## Not run: 
data("pbmc_small")
FoldChange(pbmc_small, ident.1 = 1)

## End(Not run)

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.