Runs RunTFIDF on the embedded Seurat object and
returns the updated MatisseObject. Used for ATAC-seq peak counts
in multiome datasets before RunSVD.MatisseObject.
Usage
# S3 method for class 'MatisseObject'
RunTFIDF(
object,
assay = NULL,
method = 1,
scale.factor = 10000,
idf = NULL,
verbose = TRUE,
...
)Arguments
- object
A
MatisseObject.- assay
Name of assay to use
- method
Which TF-IDF implementation to use. Choice of:
1: The TF-IDF implementation used by Stuart & Butler et al. 2019 (doi:10.1101/460147). This computes \(\log(TF \times IDF)\).
2: The TF-IDF implementation used by Cusanovich & Hill et al. 2018 (doi:10.1016/j.cell.2018.06.052). This computes \(TF \times (\log(IDF))\).
3: The log-TF method used by Andrew Hill. This computes \(\log(TF) \times \log(IDF)\).
4: The 10x Genomics method (no TF normalization). This computes \(IDF\).
- scale.factor
Which scale factor to use. Default is 10000.
- idf
A precomputed IDF vector to use. If NULL, compute based on the input data matrix.
- verbose
Print progress
- ...
Additional arguments forwarded to
RunTFIDF(e.g.assay,method).