tf_idf: Calculates the term frequency-inverse document frequency.

In jenzopr/singlecellutils: Utility functions for single-cell data

Description

Calculates the term frequency-inverse document frequency.

Usage

tf_idf(object, exprs_values = "counts", features = NULL,
  tf.method = c("raw", "binary", "adjusted", "logscaled"),
  idf.weight = c("unary", "idf", "idf.smooth", "pidf"), slot = "tfidf")

Arguments

object	A SingleCellExperiment object.
exprs_values	String indicating which assay contains the data that should be used to calculate TF-IDF.
features	A character vector (of feature names), a logical vector or numeric vector (of indices) specifying the features to use for calculation The default of NULL will use all features.
tf.method	A character vector indicating the variant for calculating the TF.
idf.weight	A character vector indicating the weighting for IDF calculation.
slot	Determines the name of the assay in assays to use for weighted expression values.

Value

A SingleCellExperiment object with modified reducedDims slot.

jenzopr/singlecellutils documentation built on June 12, 2019, 2:51 a.m.