two_source_deconv: Main function to call other subfunction to deconvolute the...

Description Usage Arguments Value Author(s) Examples

View source: R/two_source_deconv.R

Description

This is the main function that is to call all the other subfunctions and realize the deconvolution of mixed expression data. When the real mixing matrix exist, it will also compare the estimated mixing matrix and real mixing matrix and give the E1 measurement.

Usage

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two_source_deconv(ExpressionData, lowper = 0.4, highper = 0.1, epsilon1 = 0.01, epsilon2 = 0.01, A = NULL, S1=NULL, S2=NULL, return = 0)

Arguments

ExpressionData

gene expression data matrix/ExpressionSet object

lowper

The percentage of genes the user wants to remove with lowest norm. The range should be between 0 and 1.

highper

The percentage of genes the user wants to remove with highest norm.The range should be between 0 and 1.

epsilon1

Influence the number of marker genes. With increasing of epsilon1, the number marker genes in source 1 will increase. The value should be positive.

epsilon2

Influence the number of marker genes. With increasing of epsilon1, the number marker genes in source 2 will increase. The value should be positive.

A

real mixing matrix if existing

S1

Pure expression profile of first source if existing

S2

Pure expression profile of second source if existing

return

if it is equal to 0, do not return estimated S; otherwise, return the estimated S.

Value

Aest

estimated mixing matrix

E1

E1 measurement between real and estimated mixing matrix

Author(s)

Niya Wang ([email protected])

Examples

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data(NumericalMixMCF7HS27)
X <- NumericalMixMCF7HS27
deconvResult <- two_source_deconv(X, lowper = 0.4, highper = 0.1, epsilon1 = 0.1, epsilon2 = 0.1, A = NULL, S1=NULL,S2=NULL, return = 0)

Bioconductor-mirror/UNDO documentation built on June 1, 2017, 3:26 a.m.