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FoldChange

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,
  ...
)

## S3 method for class 'DimReduc'
FoldChange(
  object,
  cells.1,
  cells.2,
  features = NULL,
  slot = NULL,
  pseudocount.use = NULL,
  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. 1 by default.
base

The base with respect to which logarithms are computed.
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

data("pbmc_small")
FoldChange(pbmc_small, ident.1 = 1)
Seurat

Tools for Single Cell Genomics

v4.0.1
GPL-3 | file LICENSE
Authors
Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]
Initial release
2021-03-17

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