summary() is an analysis function that computes the protein summary
statistics for a given tidyproteomics data object. This is a passthrough function
as it returns the original tidyproteomics data-object.
Usage
# S3 method for tidyproteomics
summary(object, ...)Examples
library(dplyr, warn.conflicts = FALSE)
library(tidyproteomics)
# subset to minimize compute time
hela_subset <- hela_proteins %>% subset(description %like% 'ribosome')
#>
#> ℹ Subsetting data: description %like% ribosome
#> ✔ Subsetting data: description %like% ribosome ... done
#>
# a global summary
hela_subset %>% summary()
#>
#> ── Summary: global ──
#>
#> proteins peptides peptides_unique quantifiable CV PC1 PC2
#> 17 224 224 0.986 0.24 0.62 0.21
#>
# a summary by sample
hela_subset %>% summary("sample")
#>
#> ── Summary: sample ──
#>
#> sample proteins peptides peptides_unique quantifiable CV PC1 PC2
#> control 17 224 224 0.976 0.094 0.56 0.44
#> knockdown 17 224 224 0.996 0.170 0.75 0.25
#>
# \donttest{
# a summary by sample with imputations removed
hela_subset %>%
subset(imputed == 0) %>%
summary("sample")
#>
#> ℹ Subsetting data: imputed == 0
#> ✔ Subsetting data: imputed == 0 ... done
#>
#>
#> ── Summary: sample ──
#>
#> sample proteins peptides peptides_unique quantifiable CV PC1 PC2
#> control 17 223 223 0.976 0.097 0.61 0.39
#> knockdown 17 224 224 0.996 0.170 0.75 0.25
#>
# a summary of imputation
hela_subset %>% summary("imputed")
#>
#> ── Summary: imputed ──
#>
#> imputed proteins peptides peptides_unique quantifiable PC1 PC2 CV
#> 1 1 3 3 1.000 NA NA NA
#> 0 17 224 224 0.984 0.63 0.17 0.24
#>
hela_subset %>% summary("cellular_component")
#>
#> ── Summary: cellular_component ──
#>
#> cellular_component proteins peptides peptides_unique quantifiable CV PC1
#> Golgi 17 224 224 0.986 0.24 0.62
#> cytoskeleton 17 224 224 0.986 0.24 0.62
#> cytosol 17 224 224 0.986 0.24 0.62
#> endosome 3 23 23 0.978 0.14 0.72
#> extracellular 17 224 224 0.986 0.24 0.62
#> membrane 17 224 224 0.986 0.24 0.62
#> nucleus 17 224 224 0.986 0.24 0.62
#> PC2
#> 0.21
#> 0.21
#> 0.21
#> 0.27
#> 0.21
#> 0.21
#> 0.21
#>
hela_subset %>% summary("biological_process")
#>
#> ── Summary: biological_process ──
#>
#> biological_process proteins peptides peptides_unique
#> cell differentiation 17 224 224
#> cell growth 17 224 224
#> cell organization and biogenesis 17 224 224
#> cell proliferation 17 224 224
#> cellular component movement 17 224 224
#> cellular homeostasis 17 224 224
#> coagulation 17 224 224
#> conjugation 17 224 224
#> development 17 224 224
#> metabolic process 1 11 11
#> quantifiable CV PC1 PC2
#> 0.986 0.24 0.62 0.21
#> 0.986 0.24 0.62 0.21
#> 0.986 0.24 0.62 0.21
#> 0.986 0.24 0.62 0.21
#> 0.986 0.24 0.62 0.21
#> 0.986 0.24 0.62 0.21
#> 0.986 0.24 0.62 0.21
#> 0.986 0.24 0.62 0.21
#> 0.986 0.24 0.62 0.21
#> 0.758 0.48 NA NA
#>
# }