Create a data subset

intersection() is a specalized function for sub-setting quantitative data from a tidyproteomics data-object based data overlapping between sample groups.

Usage

intersection(data = NULL, .include = NULL, .exclude = NULL)

Arguments

data

tidyproteomics data object

.include

when exporting the "intersection" this is the set of proteins contained within the intersection of these samples

.exclude

when exporting the "intersection" this is the set of proteins found in these samples to exclude

Value

a tibble

Examples

library(dplyr, warn.conflicts = FALSE)
library(tidyproteomics)

# creates a subset of just the proteins found in 'control'
hela_proteins %>%
   subset(imputed == 0) %>%
   intersection(.include = c('control'), .exclude = c('knockdown'))
#> 
#> ℹ Subsetting data: imputed == 0
#> ✔ Subsetting data: imputed == 0 ... done
#> 
#> ℹ Intersection subset containing 60 proteins
#> 
#> ── Quantitative Proteomics Data Object ──
#> 
#> Origin          ProteomeDiscoverer 
#>                 proteins (78.40 kB) 
#> Composition     3 files 
#>                 1 samples (control) 
#> Quantitation    60 proteins 
#>                 2.9 log10 dynamic range 
#>                 9.47% missing values 
#>  *imputed        
#> Accounting      (4) num_peptides num_psms num_unique_peptides imputed 
#> Annotations     (9) description biological_process cellular_component molecular_function
#>                 gene_name wiki_pathway gene_id_ensemble gene_id_entrez
#>                 reactome_pathway 
#>