CleanCITE.gaussian.internal: Removes noise from CITE-seq protein data by fitting a...

In CamaraLab/STvEA: Spatially-resolved Transcriptomics via Epitope Anchoring

Removes noise from CITE-seq protein data by fitting a two-component Gaussian mixture to the log-normalized expression with the zeros removed, and then computing each expression measurement as the cumulative distribution of the Gaussian with the higher median.

Description

This model is similar to the one proposed by Trong et al. in the SISUA preprint (https://www.biorxiv.org/content/10.1101/631382v1)

Usage

CleanCITE.gaussian.internal(norm_cite_protein, num_cores = 1)

Arguments

norm_cite_protein	Log-normalized CITE-seq protein data (cell x protein)
num_cores	number of cores to use for parallelized fits. On Windows, this must be set to 1.

Details

Takes matrices and data frames instead of STvEA.data class

Value

Cleaned CITE-seq protein data matrix (cell x protein)

CamaraLab/STvEA documentation built on April 2, 2024, 6:07 a.m.