svmClassification: Protein subcellular localization classification

In SubCellBarCode: SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome

Description

Support Vector Machine classifier is trained and used for prediction of protein subcellular localization

Usage

svmClassification(markerProteins, protein.data, markerprot.df)

Arguments

markerProteins	character; robust marker proteins along with subcellular localization that are present in the given data.
protein.data	data.frame; fractionated proteomics data
markerprot.df	data.frame; collection of marker proteins along with corresponding subcellular localization

Value

all.classifications

Examples

{

df <- loadData(SubCellBarCode::hcc827Ctrl)

c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])

set.seed(7)
c.prots <- sample(c.prots, 500)
cls <- svmClassification(c.prots, df, markerProteins)

}

SubCellBarCode documentation built on Nov. 8, 2020, 5:26 p.m.