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Transform/normalize compartment calls using TF-IDF

Source: R/transformTFIDF.R
transformTFIDF.Rd

Transform/normalize compartment calls using TF-IDF

Usage

transformTFIDF(mat, scale.factor = 100000)

Arguments

mat

n x p input matrix (n = samples/cells; p = compartments)

scale.factor

Scaling factor for the term-frequency (TF)

Value

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

Details

This function and its helpers were modeled after or taken from:

  • http://andrewjohnhill.com/images/posts/2019-5-6-dimensionality-reduction-for-scatac-data/analysis.html

  • https://divingintogeneticsandgenomics.rbind.io/post/clustering-scatacseq-data-the-tf-idf-way/

Examples

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