Seurat: MixscapeLDA – R documentation

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MixscapeLDA

Linear discriminant analysis on pooled CRISPR screen data.

Description

This function performs unsupervised PCA on each mixscape class separately and projects each subspace onto all cells in the data. Finally, it uses the first 10 principle components from each projection as input to lda in MASS package together with mixscape class labels.

Usage

MixscapeLDA(
  object,
  assay = NULL,
  ndims.print = 1:5,
  nfeatures.print = 30,
  reduction.key = "LDA_",
  seed = 42,
  pc.assay = "PRTB",
  labels = "gene",
  nt.label = "NT",
  npcs = 10,
  verbose = TRUE,
  logfc.threshold = 0.25
)

Arguments

`object`	An object of class Seurat.
`assay`	Assay to use for performing Linear Discriminant Analysis (LDA).
`ndims.print`	Number of LDA dimensions to print.
`nfeatures.print`	Number of features to print for each LDA component.
`reduction.key`	Reduction key name.
`seed`	Value for random seed
`pc.assay`	Assay to use for running Principle components analysis.
`labels`	Meta data column with target gene class labels.
`nt.label`	Name of non-targeting cell class.
`npcs`	Number of principle components to use.
`verbose`	Print progress bar.
`logfc.threshold`	Limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Default is 0.25 Increasing logfc.threshold speeds up the function, but can miss weaker signals.

Value

Returns a Seurat object with LDA added in the reduction slot.

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