SVMDECON: Support vector machine deconvolution

In yxinyi2/ADAPTS1.0.3: Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells

Description

Use SVMDECONV to estimate the cell count percentage David L Gibbs, [e-mail] June 9, 2017

v-SVR is applied with a linear kernel to solve for f, and the best result from three values of v = 0.25, 0.5, 0.75 is saved, where ‘best’ is defined as the lowest root mean squared error between m and the deconvolution result, f x B.

Our current implementation executes v-SVR using the ‘svm’ function in the R package, ‘e1071’.

w2 <- SVMDECON(m, B)

Usage

SVMDECON(m, B)

Arguments

m	a matrix represenging the mixture (genes X 1 sample)
B	a matrix representing the references (genes X cells), m should be subset to match B

Value

A matrix with cell type estimates for each samples

yxinyi2/ADAPTS1.0.3 documentation built on Aug. 5, 2020, 12:09 a.m.