Create a data subset
subset.tidyproteomics.Rd
subset()
is the main function for sub-setting quantitative data from a tidyproteomics
data-object based on a regular expression and targeted annotation. This function
will return a smaller tidyproteomics data-object.
Note: rm.mbr()
is run as default, this is to remove MBR proteins that may no
longer have the original "anchor" observation present.
Usage
# S3 method for tidyproteomics
subset(data = NULL, ..., rm.mbr = TRUE, .verbose = TRUE)
Arguments
- data
tidyproteomics data object
- ...
a three part expression (eg. x == a)
- rm.mbr
a boolean
- .verbose
a boolean
Examples
library(dplyr, warn.conflicts = FALSE)
library(tidyproteomics)
# creates a subset of just Ribosomes, based on the string in the annotation
# protein_description
hela_proteins %>%
subset(description %like% "Ribosome") %>%
summary()
#>
#> ℹ Subsetting data: description %like% Ribosome
#> ✔ Subsetting data: description %like% Ribosome ... done
#>
#>
#> ── Summary: global ──
#>
#> proteins peptides peptides_unique quantifiable CVs
#> 18 224 224 0.986 0.24
#>
# creates a subset without Ribosomes
hela_proteins %>%
subset(!description %like% "Ribosome") %>%
summary()
#>
#> ℹ Subsetting data: !description %like% Ribosome
#> ✔ Subsetting data: !description %like% Ribosome ... done
#>
#>
#> ── Summary: global ──
#>
#> proteins peptides peptides_unique quantifiable CVs
#> 7037 66105 58482 0.908 0.25
#>