FoldChange: Fold Change

Description

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

Usage

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

Value

Returns a data.frame

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".

Examples

Run this code

if (FALSE) {
data("pbmc_small")
FoldChange(pbmc_small, ident.1 = 1)
}