deconLNR: Deconvolution using logNormReg package to run linear mean...

In SpatialDecon: Deconvolution of mixed cells from spatial and/or bulk gene expression data

Description

Calls lognlm() to optimize the model.

Usage

deconLNR(Y, X, bg = 0, weights = NULL, epsilon = NULL, maxit = 1000)

Arguments

Y	p-length expression vector or p * N expression matrix - the actual (linear-scale) data
X	p * K Training matrix
bg	scalar or matrix of expected background counts per data point.
weights	The same as the weights argument used by lm
epsilon	optional, a very small non-zero number to use as a lower threshold to make fits well-behaved
maxit	Maximum number of iterations. Default 1000.

Value

a list: beta (estimate), sigmas (covariance matrix of estimate, derived by inverting the hessian from lognlm)

SpatialDecon documentation built on Nov. 8, 2020, 6 p.m.