tfidf: TF-IDF normalization

In plantformatics/Socrates: Analysis of scATAC-seq data

TF-IDF normalization

Description

Run TF-IDF on binary cell x peak matrix. Returns normalized TF-IDF values in the residuals slot. Code adapted from Andrew Hill (http://andrewjohnhill.com/blog/2019/05/06/dimensionality-reduction-for-scatac-data/).

Usage

tfidf(
  obj,
  frequencies = T,
  log_scale_tf = T,
  scale_factor = 10000,
  doL2 = F,
  slotName = "residuals"
)

Arguments

obj	list object containing dgCMatrix in 'counts' slot.
frequencies	logical, whether to scale matrix by barcode peak sums. Defaults to TRUE.
log_scale_tf	logical, whether to log1p transform the term frequency (TF). Defaults to TRUE.
scale_factor	numeric,
doL2	logical, whether or not to L2 normalize TFIDF values (per cell). Defaults to FALSE.
slotName	character, specify the slot name for saving residuals. Useful for saving multiple normalization steps. Note, make sure to update the slotName argument for downstream functions. Defaults to "residuals".

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.