Seurat: ScoreJackStraw – R documentation

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ScoreJackStraw

Compute Jackstraw scores significance.

Description

Significant PCs should show a p-value distribution that is strongly skewed to the left compared to the null distribution. The p-value for each PC is based on a proportion test comparing the number of features with a p-value below a particular threshold (score.thresh), compared with the proportion of features expected under a uniform distribution of p-values.

Usage

ScoreJackStraw(object, ...)

## S3 method for class 'JackStrawData'
ScoreJackStraw(object, dims = 1:5, score.thresh = 1e-05, ...)

## S3 method for class 'DimReduc'
ScoreJackStraw(object, dims = 1:5, score.thresh = 1e-05, ...)

## S3 method for class 'Seurat'
ScoreJackStraw(
  object,
  reduction = "pca",
  dims = 1:5,
  score.thresh = 1e-05,
  do.plot = FALSE,
  ...
)

Arguments

`object`	An object
`...`	Arguments passed to other methods
`dims`	Which dimensions to examine
`score.thresh`	Threshold to use for the proportion test of PC significance (see Details)
`reduction`	Reduction associated with JackStraw to score
`do.plot`	Show plot. To return ggplot object, use `JackStrawPlot` after running ScoreJackStraw.

Value

Returns a Seurat object

Author(s)

Omri Wurtzel

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

ScoreJackStraw

Description

Usage

Arguments

Value

Author(s)

See Also

Seurat

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