Make unique names
make_unique.Rdmake_unique generates unique identifiers
for a proteomics dataset based on "name" and "id" columns.
Arguments
- proteins
Data.frame, Protein table for which unique names will be created.
- names
Character(1), Name of the column containing feature names.
- ids
Character(1), Name of the column containing feature IDs.
- delim
Character(1), Sets the delimiter separating the feature names within one protein group.
Value
A data.frame with the additional variables "name" and "ID" containing unique names and identifiers, respectively.
Examples
# Load example
data(Silicosis_pg)
data <- Silicosis_pg
# Check colnames and pick the appropriate columns
colnames(data)
#> [1] "Protein.IDs" "Majority.protein.IDs"
#> [3] "Peptide.counts..all." "Peptide.counts..razor.unique."
#> [5] "Peptide.counts..unique." "Protein.names"
#> [7] "Gene.names" "Fasta.headers"
#> [9] "Number.of.proteins" "Peptides"
#> [11] "Razor...unique.peptides" "Unique.peptides"
#> [13] "iBAQ.PBS_1" "iBAQ.PBS_2"
#> [15] "iBAQ.PBS_3" "iBAQ.PBS_4"
#> [17] "iBAQ.W10_2" "iBAQ.W10_4"
#> [19] "iBAQ.W2_1" "iBAQ.W2_3"
#> [21] "iBAQ.W2_4" "iBAQ.W2_5"
#> [23] "iBAQ.W4_2" "iBAQ.W4_3"
#> [25] "iBAQ.W4_4" "iBAQ.W4_5"
#> [27] "iBAQ.W6_2" "iBAQ.W6_3"
#> [29] "iBAQ.W6_4" "iBAQ.W6_6"
#> [31] "iBAQ.W9_2" "iBAQ.W9_4"
#> [33] "LFQ.intensity.PBS_1" "LFQ.intensity.PBS_2"
#> [35] "LFQ.intensity.PBS_3" "LFQ.intensity.PBS_4"
#> [37] "LFQ.intensity.W10_2" "LFQ.intensity.W10_4"
#> [39] "LFQ.intensity.W2_1" "LFQ.intensity.W2_3"
#> [41] "LFQ.intensity.W2_4" "LFQ.intensity.W2_5"
#> [43] "LFQ.intensity.W4_2" "LFQ.intensity.W4_3"
#> [45] "LFQ.intensity.W4_4" "LFQ.intensity.W4_5"
#> [47] "LFQ.intensity.W6_2" "LFQ.intensity.W6_3"
#> [49] "LFQ.intensity.W6_4" "LFQ.intensity.W6_6"
#> [51] "LFQ.intensity.W9_2" "LFQ.intensity.W9_4"
#> [53] "Only.identified.by.site" "Reverse"
#> [55] "Potential.contaminant"
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")