Signac (version 0.2.4)

RunTFIDF: Compute the term-frequency inverse-document-frequency

Description

Run term frequency inverse document frequency (TF-IDF) normalization

Usage

RunTFIDF(object, ...)
# S3 method for default
RunTFIDF(
  object,
  assay = NULL,
  method = 1,
  scale.factor = 10000,
  verbose = TRUE,
  ...
)
# S3 method for Assay
RunTFIDF(
  object,
  assay = NULL,
  method = 1,
  scale.factor = 10000,
  verbose = TRUE,
  ...
)
# S3 method for Seurat
RunTFIDF(
  object,
  assay = NULL,
  method = 1,
  scale.factor = 10000,
  verbose = TRUE,
  ...
)

Arguments

object

A Seurat object

...

Arguments passed to other methods

assay

Name of assay to use

method

Which TF-IDF implementation to use. Choice of:

• 1: The LSI implementation used by Stuart & Butler et al. 2019 (https://doi.org/10.1101/460147).

• 2: The standard LSI implementation used by Cusanovich & Hill et al. 2018 (https://doi.org/10.1016/j.cell.2018.06.052).

• 3: The log-TF method

• 4: The 10x Genomics method (no TF normalization)

scale.factor

Which scale factor to use. Default is 10000.

verbose

Print progress

Value

Returns a Seurat object

Examples

# NOT RUN {
mat <- matrix(data = rbinom(n = 25, size = 5, prob = 0.2), nrow = 5)
RunTFIDF(object = mat)
RunTFIDF(atac_small[['peaks']])
RunTFIDF(object = atac_small)
# }