ModelNegativeADTnorm function

ModelNegativeADTnorm R function: Normalize single cell antibody derived tag (ADT) protein data. This function defines the background level for each protein by fitting a 2 component Gaussian mixture after log transformation. Empty Droplet ADT counts are not supplied. The fitted background mean of each protein across all cells is subtracted from the log transformed counts. Note this is distinct from and unrelated to the 2 component mixture used in the second step of DSBNormalizeProtein which is fitted to all proteins of each cell. After this background correction step, ModelNegativeADTnorm then models and removes technical cell to cell variations using the same step II procedure as in the DSBNormalizeProtein function using identical function arguments. This is a experimental function that performs well in testing and is motivated by our observation in Supplementary Fig 1 in the dsb paper showing that the fitted background mean was concordant with the mean of ambient ADTs in both empty droplets and unstained control cells. We recommend using ModelNegativeADTnorm if empty droplets are not available. See https://www.nature.com/articles/s41467-022-29356-8 for details of the algorithm.

  • Maintainer: Matthew Mulè
  • License: CC0 | file LICENSE
  • Last published: 2025-04-02