projectCellTypeWithError: Estimate cellular composition with error
In ds420/CETYGO: Quantifying the accuracy of cellular deconvolution

View source: R/projectCellTypeWithError.R

projectCellTypeWithError

R Documentation

Estimate cellular composition with error

Description

Estimate the cellular composition from a DNA methylation profile and calculate the CETYGO score error metric associated with this estimate.

Usage

projectCellTypeWithError(YIN, coefs)

Arguments

`YIN`	a matrix of DNA methylation levels from the samples that require cell composition to be estimated.
`coefs`	A matrix of deconvolution model parameters including coefficients. This input can be generated with the pickCompProbesMatrix()$coefs

Value

A matrix with the estimated proportion of cell types, CETYGO and the number of sites missing from the model.

Examples

# using pre-trained model for whole blood provided with the package and
# sample whole blood profiles
rInd <- rownames(bulkdata)[rownames(bulkdata) %in% rownames(modelBloodCoef)]
predProp <- projectCellTypeWithError(bulkdata, modelBloodCoef[rInd, ])

head(predProp)

ds420/CETYGO documentation built on July 7, 2023, 12:16 a.m.