ambientProfileBimodal {DropletUtils} | R Documentation

## Ambient profile from bimodality

### Description

Estimate the concentration of each feature in the ambient solution from a filtered count matrix containing only counts for cells, by assuming that each feature has a bimodal abundance distribution with ambient and high-expressing components.

### Usage

    inferAmbience(...)

    ambientProfileBimodal(x, ...)

    ## S4 method for signature 'ANY'
    ambientProfileBimodal(x, min.prop = 0.05)

    ## S4 method for signature 'SummarizedExperiment'
    ambientProfileBimodal(x, ..., assay.type = "counts")

### Arguments

`...` | For the generic, further arguments to pass to individual methods. For the SummarizedExperiment method, further arguments to pass to the ANY method. For `inferAmbience`, arguments to pass to `ambientProfileBimodal`.
`x` | A numeric matrix-like object containing counts for each feature (row) and cell (column). Alternatively, a SummarizedExperiment object containing such a matrix.
`min.prop` | Numeric scalar in (0, 1) specifying the expected minimum proportion of barcodes contributed by each sample.
`assay.type` | Integer or scalar specifying the assay containing the count matrix.

### Details

In some cases, we want to know the ambient profile but we only have the count matrix for the cell-containing libraries. This can be useful in functions such as `hashedDrops` or as a reference profile in `medianSizeFactors`. However, as we only have the cell-containing libraries, we cannot use `ambientProfileEmpty`.

This function estimates the ambient profile by assuming that each feature only labels a minority of the cells. Under this assumption, each feature's log-count distribution has a bimodal distribution where the lower mode represents ambient contamination. This is generally reasonable for tag-based applications like cell hashing or CITE-seq where data is usually binary, i.e., the marker is either present or not. We fit a two-component mixture model and identify all barcodes assigned to the lower component; and the mean of those counts is used as an estimate of the ambient contribution.

The initialization of the mixture model is controlled by `min.prop`, which starts the means of the lower and upper components at the `min.prop` and `1-min.prop` quantiles, respectively. This means that each sample is expected to contribute somewhere between `[min.prop, 1-min.prop]` barcodes. Larger values improve convergence but require stronger assumptions about the relative proportions of multiplexed samples.

`inferAmbience` is soft-deprecated; use `ambientProfileBimodal` instead.

### Value

A numeric vector of length equal to `nrow(x)`, containing the estimated ambient proportions for each feature.

### Author(s)

Aaron Lun

### See Also

`hashedDrops`, where this function is used in the absence of an ambient profile.

`ambientProfileEmpty`, which should be used when the raw matrix (prior to filtering for cells) is available.

`ambientContribSparse` and related functions, to estimate the contribution of ambient contamination in each library.

### Examples

    x <- rbind(
        rpois(1000, rep(c(100, 1), c(100, 900))),
        rpois(1000, rep(c(2, 100, 2), c(100, 100, 800))),
        rpois(1000, rep(c(3, 100, 3), c(200, 700, 100)))
    )

    # Should be close to 1, 2, 3
    ambientProfileBimodal(x)

[Package DropletUtils version 1.14.2 Index]