simple_FNR_params {scone} | R Documentation

## Fit Simple False-Negative Model

### Description

Fits a logistic regression model of false negative observations as a function of expression level, using a set of positive control (ubiquitously expressed) genes

### Usage

    simple_FNR_params(expr, pos_controls, fn_tresh = 0.01)

### Arguments

`expr` | matrix A matrix of transcript-proportional units (genes in rows, cells in columns).
`pos_controls` | A logical, numeric, or character vector indicating control genes that will be used to compute false-negative rate characteristics. User must provide at least 2 control genes.
`fn_tresh` | Inclusive threshold for negative detection. Default 0.01. fn_tresh must be non-negative.

### Details

logit(Probability of False Negative) ~ a + b*(median log-expr)

### Value

A matrix of logistic regression coefficients corresponding to glm fits in each sample (a and b in columns 1 and 2 respectively). If the a & b fit does not converge, b is set to zero and only a is estimated.

### Examples

    mat <- matrix(rpois(1000, lambda = 3), ncol=10)
    mat = mat * matrix(1-rbinom(1000, size = 1, prob = .01), ncol=10)
    fnr_out = simple_FNR_params(mat,pos_controls = 1:10)

[Package scone version 1.16.1 Index]