escoEstBCV: Estimate esco Biological Coefficient of Variation parameters

Description Usage Arguments Details Value

View source: R/esco-estimate.R

Description

Parameters are estimated using the estimateDisp function in the edgeR package.

Usage

1
escoEstBCV(counts, norm.counts, params, cellinfo = NULL)

Arguments

counts

counts matrix to estimate parameters from.

norm.counts

normalized counts matrix to estimate parameters from.

params

escoParams object to store estimated values in.

cellinfo

info about the identity of each cell in the cell structure. If cellinfo is not null, then BCV is estiamted adjusted to the cell structures

Details

The estimateDisp function is used to estimate the common dispersion and prior degrees of freedom. See estimateDisp for details. When estimating parameters on simulated data we found a broadly linear relationship between the true underlying common dispersion and the edgR estimate, therefore we apply a small correction, disp = 0.1 + 0.25 * edgeR.disp.

Value

escoParams object with estimated values.


JINJINT/ESCO documentation built on May 13, 2021, 7:25 p.m.