compareCls {SubCellBarCode}R Documentation

Compare exon and gene centric classifications

Description

Comparison of the gene centric and exon centric classification. Additionally, correlation analysis is performed using quantification data.

Usage

compareCls(geneCls, exonCls)

Arguments

geneCls,

data frame gene centric classification output

exonCls,

data frame exon centric classification output

Value

c.df

Examples

{

exon.cls <- data.frame(Protein = c("ENSE00000331854",
                                     "ENSE00000331855",
                                     "ENSE00000331859"),
                         NeighborhoodCls = c("Cytosol",
                                      "Cytosol",
                                      "Cytosol"),
                         CompartmentCls = c("C1","C1","C1"),
                         Secretory = c(0.1, 0.1, 0.1),
                         Nuclear = c(0.2, 0.2, 0.2),
                         Cytosol = c(0.2, 0.2, 0.2),
                         Mitochondria = c(0.2, 0.2, 0.2),
                         S1 = c(0.2, 0.2, 0.2),
                         S2 = c(0.2, 0.2, 0.2),
                         S3 = c(0.2, 0.2, 0.2),
                         S4 = c(0.2, 0.2, 0.2),
                         N1 = c(0.2, 0.2, 0.2),
                         N2 = c(0.2, 0.2, 0.2),
                         N3 = c(0.2, 0.2, 0.2),
                         N4 = c(0.2, 0.2, 0.2),
                         C1 = c(0.2, 0.2, 0.2),
                         C2 = c(0.2, 0.2, 0.2),
                         C3 = c(0.2, 0.2, 0.2),
                         C4 = c(0.2, 0.2, 0.2),
                         C5 = c(0.2, 0.2, 0.2),
                         M1 = c(0.2, 0.2, 0.2),
                         M2 = c(0.2, 0.2, 0.2),
                         GeneSymbol = c("COPB1", "COPB1", "COPB1"),
                         PeptideCount = c(2, 4, 7))

gene.cls <- data.frame(Protein = c("COPB1"),
NeighborhoodCls = c("Cytosol"),
CompartmentCls = c("C1"),
Secretory = c(0.1),
Nuclear = c(0.2),
Cytosol = c(0.2),
Mitochondria = c(0.2),
S1 = c(0.2),
S2 = c(0.2),
S3 = c(0.2),
S4 = c(0.2),
N1 = c(0.2),
N2 = c(0.2),
N3 = c(0.2),
N4 = c(0.2),
C1 = c(0.2),
C2 = c(0.2),
C3 = c(0.2),
C4 = c(0.2),
C5 = c(0.2),
M1 = c(0.2),
M2 = c(0.2))

comp.df <- compareCls(gene.cls, exon.cls)

}

[Package SubCellBarCode version 1.6.0 Index]