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Filter Samples or Variables of an Experiment

filter_obs.Rd

Getting a subset of an experiment() by filtering samples or variables.

The same syntax as dplyr::filter() is used. For example, to get a subset of an experiment keeping only "HC" samples, use filter_obs(exp, group == "HC"). This actually calls dplyr::filter() on the sample information tibble with condition group == "HC", and then updates the expression matrix accordingly.

If no samples or variables are left after filtering, an error is thrown.

Usage

filter_obs(exp, ...)

filter_var(exp, ...)

Arguments

exp

An experiment().

...

<data-masking> Expression to filter samples or variables. passed to dplyr::filter() internally.

Value

An new experiment() object.

Examples

library(magrittr)

# Create a toy experiment for demonstration
exp <- toy_experiment()
# Add a type column to the variable information for demonstration
exp$var_info$type <- c("X", "X", "Y", "Y")

# Filter samples
sub_exp_1 <- filter_obs(exp, group == "A")
get_sample_info(sub_exp_1)
#> # A tibble: 3 × 3
#>   sample group batch
#>   <chr>  <chr> <dbl>
#> 1 S1     A         1
#> 2 S2     A         2
#> 3 S3     A         1
get_expr_mat(sub_exp_1)
#>    S1 S2 S3
#> V1  1  5  9
#> V2  2  6 10
#> V3  3  7 11
#> V4  4  8 12

# Filter variables
sub_exp_2 <- filter_var(exp, type == "X")
get_var_info(sub_exp_2)
#> # A tibble: 2 × 5
#>   variable protein peptide glycan_composition type 
#>   <chr>    <chr>   <chr>   <chr>              <chr>
#> 1 V1       PRO1    PEP1    H5N2               X    
#> 2 V2       PRO2    PEP2    H5N2               X    
get_expr_mat(sub_exp_2)
#>    S1 S2 S3 S4 S5 S6
#> V1  1  5  9 13 17 21
#> V2  2  6 10 14 18 22

# Use pipe
sub_exp_3 <- exp %>%
  filter_obs(group == "A") %>%
  filter_var(type == "X")
get_sample_info(sub_exp_3)
#> # A tibble: 3 × 3
#>   sample group batch
#>   <chr>  <chr> <dbl>
#> 1 S1     A         1
#> 2 S2     A         2
#> 3 S3     A         1
get_var_info(sub_exp_3)
#> # A tibble: 2 × 5
#>   variable protein peptide glycan_composition type 
#>   <chr>    <chr>   <chr>   <chr>              <chr>
#> 1 V1       PRO1    PEP1    H5N2               X    
#> 2 V2       PRO2    PEP2    H5N2               X    
get_expr_mat(sub_exp_3)
#>    S1 S2 S3
#> V1  1  5  9
#> V2  2  6 10