hdf5TFIDF: Transform/normalize compartment calls using TF-IDF on...

View source: R/transformTFIDF.R

hdf5TFIDFR Documentation

Transform/normalize compartment calls using TF-IDF on HDF5-backed objects

Description

Transform/normalize compartment calls using TF-IDF on HDF5-backed objects

Usage

hdf5TFIDF(h5, scale.factor = 1e+05, return.dense = FALSE, return.se = FALSE)

Arguments

h5

SummarizedExperiment object, DelayedMatrix, or a normal matrix

scale.factor

Scaling factor for the term-frequency (TF)

return.dense

Whether to return a dense, in memory matrix

return.se

Whether to return the TF-IDF matrix as a new assay in the SummarizedExperiment

Value

A TF-IDF transformed matrix of the same dimensions as the input

Examples


m <- 1000
n <- 100
mat <- round(matrix(runif(m*n), m, n))
#Input needs to be a tall matrix
tfidf <- hdf5TFIDF(mat)


biobenkj/compartmap documentation built on Oct. 18, 2023, 11:11 a.m.