compareCls: Compare exon and gene centric classifications

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

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)

}

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