Summarize the data
summary.tidyproteomics.Rdsummary() 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)
# a global summary
hela_proteins %>% summary()
#>
#> ── Summary: global ──
#>
#> proteins peptides peptides_unique quantifiable CVs
#> 7055 66329 58706 0.908 0.25
#>
# a summary by sample
hela_proteins %>% summary("sample")
#>
#> ── Summary: sample ──
#>
#> sample proteins peptides peptides_unique quantifiable CVs
#> control 7055 66329 58706 0.908 0.16
#> knockdown 7055 66329 58706 0.909 0.21
#>
# a summary by sample with imputations removed
hela_proteins %>%
subset(imputed == 0) %>%
summary("sample")
#>
#> ℹ Subsetting data: imputed == 0
#> ✔ Subsetting data: imputed == 0 ... done
#>
#>
#> ── Summary: sample ──
#>
#> sample proteins peptides peptides_unique quantifiable CVs
#> control 7002 65418 58151 0.907 0.16
#> knockdown 6995 65588 58254 0.908 0.21
#>
# a summary of imputation
hela_proteins %>% summary("imputed")
#>
#> ── Summary: imputed ──
#>
#> imputed proteins peptides peptides_unique quantifiable CVs
#> 1 695 827 504 0.999 0.24
#> 0 7055 65503 58203 0.907 0.25
#>
hela_proteins %>% summary("cellular_component")
#>
#> ── Summary: cellular_component ──
#>
#> cellular_component proteins peptides peptides_unique quantifiable CVs
#> Golgi 9 44 35 0.902 0.200
#> cell surface 18 52 52 0.712 0.275
#> chromosome 3 6 6 0.111 0.320
#> cytoplasm 7055 66329 58706 0.908 0.250
#> cytoskeleton 127 504 422 0.691 0.280
#> cytosol 121 1275 1208 0.935 0.240
#> endoplasmic reticulum 24 182 75 0.776 0.220
#> endosome 111 975 883 0.907 0.240
#> extracellular 33 341 296 0.819 0.310
#> membrane 431 4082 3535 0.890 0.250
#> mitochondrion 16 88 87 0.831 0.310
#> nucleus 186 1169 959 0.843 0.280
#>
hela_proteins %>% summary("biological_process")
#>
#> ── Summary: biological_process ──
#>
#> biological_process proteins peptides peptides_unique
#> cell communication 9 100 93
#> cell death 1 3 1
#> cell differentiation 3 9 9
#> cell growth 104 1419 839
#> cell organization and biogenesis 17 241 241
#> cell proliferation 7055 66329 58706
#> cellular component movement 6 13 11
#> cellular homeostasis 324 2854 2631
#> coagulation 9 68 58
#> conjugation 181 1460 1240
#> defense response 15 83 76
#> development 38 180 164
#> metabolic process 342 2804 2422
#> quantifiable CVs
#> 0.920 0.200
#> 1.000 0.340
#> 0.389 0.305
#> 0.803 0.280
#> 0.967 0.210
#> 0.908 0.250
#> 0.679 0.410
#> 0.938 0.260
#> 0.885 0.220
#> 0.893 0.260
#> 0.709 0.275
#> 0.730 0.245
#> 0.886 0.250
#>