Filter GroupIds — filter_groupIds • claman

Remove all data besides those from provided groupIds

filter_groupIds(mzroll_list, groupIds, invert = FALSE)

Arguments

mzroll_list	output of process_mzroll or process_mzroll_multi features: one row per unique analyte (defined by a unique groupId), samples: one row per unique sample (defined by a unique sampleId), measurements: one row per peak (samples x peakgroups)
groupIds	groupIds to retain
invert	if TRUE then remove provided groupIds; if FALSE then retain provided groupIds

mzroll_list

output of process_mzroll or process_mzroll_multi

features: one row per unique analyte (defined by a unique groupId),
samples: one row per unique sample (defined by a unique sampleId),
measurements: one row per peak (samples x peakgroups)

groupIds

groupIds to retain

invert

if TRUE then remove provided groupIds; if FALSE then retain provided groupIds

Examples

filter_groupIds(nplug_mzroll_normalized, factor(1:10))
#> $features
#> # A tibble: 10 × 13
#>    groupId compoundName       smiles adductName tagString    mz    rt compoundDB
#>    <fct>   <chr>              <chr>  <chr>      <chr>     <dbl> <dbl> <chr>     
#>  1 1       Ribose-P           NA     NA         ""           NA    NA NA        
#>  2 2       OMP                NA     NA         ""           NA    NA NA        
#>  3 3       1,3-diphopshategl… NA     NA         ""           NA    NA NA        
#>  4 4       3-hydroxy-3-methy… NA     NA         ""           NA    NA NA        
#>  5 5       3-phosphoglycerate NA     NA         ""           NA    NA NA        
#>  6 6       6-phospho-D-gluco… NA     NA         ""           NA    NA NA        
#>  7 7       acetyl-CoA         NA     NA         ""           NA    NA NA        
#>  8 8       aconitate          NA     NA         ""           NA    NA NA        
#>  9 9       adenosine          NA     NA         ""           NA    NA NA        
#> 10 10      ADP                NA     NA         ""           NA    NA NA        
#> # … with 5 more variables: searchTableName <chr>, label <chr>,
#> #   peak_label <chr>, method_tag <chr>, pathway <chr>
#> 
#> $samples
#> # A tibble: 26 × 4
#>    sampleId limitation    DR name   
#>    <fct>    <chr>      <dbl> <glue> 
#>  1 1        NH4        0.055 N0.06  
#>  2 3        NH4        0.173 N0.17  
#>  3 5        NH4        0.21  N0.21  
#>  4 7        NH4        0.29  N0.29  
#>  5 9        URA        0.056 U0.06  
#>  6 11       URA        0.11  U0.11  
#>  7 13       URA        0.15  U0.15  
#>  8 15       URA        0.22  U0.22  
#>  9 17       URA        0.31  U0.31  
#> 10 19       PO4        0.056 P0.06-1
#> # … with 16 more rows
#> 
#> $measurements
#> # A tibble: 260 × 5
#>    groupId sampleId log2_abundance centered_log2_abundan… normalized_log2_abund…
#>    <fct>   <fct>             <dbl>                  <dbl>                  <dbl>
#>  1 1       1                  15.0                  1.14                  0.812 
#>  2 1       3                  15.5                  1.62                  1.30  
#>  3 1       5                  15.5                  1.61                  1.29  
#>  4 1       7                  16.1                  2.27                  1.94  
#>  5 1       9                  13.8                 -0.105                -0.430 
#>  6 1       11                 14.3                  0.409                 0.0841
#>  7 1       13                 14.8                  0.931                 0.606 
#>  8 1       15                 15.5                  1.61                  1.28  
#>  9 1       17                 16.1                  2.21                  1.89  
#> 10 1       19                 10.6                 -3.25                 -2.81  
#> # … with 250 more rows
#> 
#> $design
#> $design$features
#> # A tibble: 13 × 2
#>    variable        type               
#>    <chr>           <chr>              
#>  1 groupId         feature_primary_key
#>  2 compoundName    character          
#>  3 smiles          character          
#>  4 adductName      character          
#>  5 tagString       character          
#>  6 mz              numeric            
#>  7 rt              numeric            
#>  8 compoundDB      character          
#>  9 searchTableName character          
#> 10 label           character          
#> 11 peak_label      character          
#> 12 method_tag      character          
#> 13 pathway         character          
#> 
#> $design$samples
#> # A tibble: 4 × 2
#>   variable   type              
#>   <chr>      <chr>             
#> 1 sampleId   sample_primary_key
#> 2 limitation character         
#> 3 DR         numeric           
#> 4 name       glue              
#> 
#> $design$measurements
#> # A tibble: 5 × 2
#>   variable                  type               
#>   <chr>                     <chr>              
#> 1 groupId                   feature_primary_key
#> 2 sampleId                  sample_primary_key 
#> 3 log2_abundance            numeric            
#> 4 centered_log2_abundance   numeric            
#> 5 normalized_log2_abundance numeric            
#> 
#> $design$feature_pk
#> [1] "groupId"
#> 
#> $design$sample_pk
#> [1] "sampleId"
#> 
#> 
#> attr(,"class")
#> [1] "triple_omic" "tomic"       "mzroll"