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

In biobenkj/compartmentalizer: Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

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/compartmentalizer documentation built on Oct. 13, 2023, 5:26 p.m.