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Select Columns of the Sample or Variable Information Tibble

select_obs.Rd

These two functions provide a way to trimming down the sample or variable information tibble of an experiment() to only the columns of interest.

The same syntax as dplyr::select() is used. For example, to get a new experiment() with only the "sample" and "group" columns in the sample information tibble, use select_obs(exp, group). Note that you don't need to (and you can't) explicitly select or deselect the sample column in sample_info. It is automatically handled by select_obs(), always being selected. The same applies to the variable column in var_info.

Usage

select_obs(exp, ...)

select_var(exp, ...)

Arguments

exp

An experiment().

...

<data-masking> Column names to select. If empty, all columns except the sample or variable column will be discarded.

Value

An new experiment() object.

Details

When using select_var() with dplyr, you may encounter package conflicts. dplyr also has a function called select_var() that has been deprecated for over two years. If you encounter package conflicts, use the following code to resolve them:

conflicted::conflicts_prefer(glyexp::select_var)
#> [conflicted] Removing existing preference.
#> [conflicted] Will prefer glyexp::select_var over any other package.

Examples

library(magrittr)

toy_exp <- toy_experiment()

toy_exp_2 <- toy_exp %>%
  select_obs(group) %>%
  select_var(protein, peptide)

get_sample_info(toy_exp_2)
#> # A tibble: 6 × 2
#>   sample group
#>   <chr>  <chr>
#> 1 S1     A    
#> 2 S2     A    
#> 3 S3     A    
#> 4 S4     B    
#> 5 S5     B    
#> 6 S6     B    
get_var_info(toy_exp_2)
#> # A tibble: 4 × 3
#>   variable protein peptide
#>   <chr>    <chr>   <chr>  
#> 1 V1       PRO1    PEP1   
#> 2 V2       PRO2    PEP2   
#> 3 V3       PRO3    PEP3   
#> 4 V4       PRO3    PEP4