Seurat (version 3.1.4)

RunLSI: Run Latent Semantic Indexing on binary count matrix

Description

For details about stored LSI calculation parameters, see PrintLSIParams.

Usage

RunLSI(object, ...)
# S3 method for default
RunLSI(
  object,
  assay = NULL,
  n = 50,
  reduction.key = "LSI_",
  scale.max = NULL,
  seed.use = 42,
  verbose = TRUE,
  ...
)
# S3 method for Assay
RunLSI(
  object,
  assay = NULL,
  features = NULL,
  n = 50,
  reduction.key = "LSI_",
  scale.max = NULL,
  verbose = TRUE,
  ...
)
# S3 method for Seurat
RunLSI(
  object,
  assay = NULL,
  features = NULL,
  n = 50,
  reduction.key = "LSI_",
  reduction.name = "lsi",
  scale.max = NULL,
  verbose = TRUE,
  ...
)

Arguments

object

Seurat object

...

Arguments passed to other methods

assay

Which assay to use. If NULL, use the default assay

n

Number of singular values to compute

reduction.key

Key for dimension reduction object

scale.max

Clipping value for cell embeddings. Default (NULL) is no clipping.

seed.use

Set a random seed. By default, sets the seed to 42. Setting NULL will not set a seed.

verbose

Print messages

features

Which features to use. If NULL, use variable features

reduction.name

Name for stored dimension reduction object. Default 'lsi'

Examples

# NOT RUN {
lsi <- RunLSI(object = pbmc_small, n = 5)

# }