mergeCls: Merge compartment and neighborhood classification

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

Description

Compartment and neighborhood classifications are merged for the single output.

Usage

mergeCls(compartmentCls, neighborhoodCls)

Arguments

compartmentCls	data.frame; all predictions, including unclassified as well, and probablity vectors for each protein in compartment classification
neighborhoodCls	data.frame; all predictions, including unclassified as well, and probablity vectors for each protein in compartment classification

Value

cls.df

Examples

{

#create mock data
com.df <- data.frame(Proteins = "TP53",
svm.pred = "N1",
S1 = as.numeric(0.02),
S2 = as.numeric(0.02),
S3 = as.numeric(0.02),
S4 = as.numeric(0.02),
N1 = as.numeric(0.72),
N2 = as.numeric(0.02),
N3 = as.numeric(0.02),
N4 = as.numeric(0.02),
C1 = as.numeric(0.02),
C2 = as.numeric(0.02),
C3 = as.numeric(0.02),
C4 = as.numeric(0.02),
C5 = as.numeric(0.02),
M1 = as.numeric(0.02),
M2 = as.numeric(0.02))

rownames(com.df) <- "TP53"

neig.df <- data.frame(Proteins = "TP53",
svm.pred.all = "Nuclear",
Secretory = as.numeric(0.01),
Nuclear = as.numeric(0.95),
Cytosol = as.numeric(0.02),
Mitochondria = as.numeric(0.02))

rownames(neig.df) <- "TP53"

cls.df <- mergeCls(com.df, neig.df)

}

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