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R
Seurat

subset.AnchorSet

Subset an AnchorSet object

Description

Subset an AnchorSet object

Usage

## S3 method for class 'AnchorSet'
subset(
  x,
  score.threshold = NULL,
  disallowed.dataset.pairs = NULL,
  dataset.matrix = NULL,
  group.by = NULL,
  disallowed.ident.pairs = NULL,
  ident.matrix = NULL,
  ...
)

Arguments

x

object to be subsetted.
score.threshold

Only anchor pairs with scores greater than this value are retained.
disallowed.dataset.pairs

Remove any anchors formed between the provided pairs. E.g. list(c(1, 5), c(1, 2)) filters out any anchors between datasets 1 and 5 and datasets 1 and 2.
dataset.matrix

Provide a binary matrix specifying whether a dataset pair is allowable (1) or not (0). Should be a dataset x dataset matrix.
group.by

Grouping variable to determine allowable ident pairs
disallowed.ident.pairs

Remove any anchors formed between provided ident pairs. E.g. list(c("CD4", "CD8"), c("B-cell", "T-cell"))
ident.matrix

Provide a binary matrix specifying whether an ident pair is allowable (1) or not (0). Should be an ident x ident symmetric matrix
...

further arguments to be passed to or from other methods.

Value

Returns an AnchorSet object with specified anchors filtered out

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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