Subset an AnchorSet object

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