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

Description Usage Arguments Value Examples

View source: R/transformTFIDF.R

Description

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

Usage

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hdf5TFIDF(h5, scale.factor = 100000, 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

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

JordanVeldboom/compartmap documentation built on July 3, 2020, 6:32 p.m.