process_mzroll.RdProcess mzRoll
process_mzroll( mzroll_db_path, only_identified = TRUE, validate = FALSE, method_tag = "" )
| mzroll_db_path | path to mzroll DB file |
|---|---|
| only_identified | TRUE/FALSE, filter to only features which were identified. |
| validate | TRUE/FALSE, use meta-data to only name the subset of features which were manually validated. |
| method_tag | what method was run (for the purpose of matching meta-data and aggregating). |
a **triple_omic** from **romic** containing three tibbles:
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)
And, a design list which tracks the variables in each table.
#> $features #> # A tibble: 106 × 12 #> 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 96 more rows, and 4 more variables: searchTableName <chr>, #> # label <chr>, peak_label <chr>, method_tag <chr> #> #> $samples #> # A tibble: 136 × 3 #> sampleId name filename #> <fct> <chr> <chr> #> 1 1 NH4_0.055_filter_b NA #> 2 2 NH4_0.055_filter_d NA #> 3 3 NH4_0.055_pellet_a NA #> 4 4 NH4_0.055_pellet_c NA #> 5 5 NH4_0.173_filter_b NA #> 6 6 NH4_0.173_filter_d NA #> 7 7 NH4_0.173_pellet_a NA #> 8 8 NH4_0.173_pellet_c NA #> 9 9 NH4_0.210_filter_b NA #> 10 10 NH4_0.210_filter_d NA #> # … with 126 more rows #> #> $measurements #> # A tibble: 14,416 × 4 #> groupId sampleId log2_abundance centered_log2_abundance #> <fct> <fct> <dbl> <dbl> #> 1 2 1 8.23 -1.27 #> 2 4 1 8.23 -0.816 #> 3 15 1 8.23 -4.60 #> 4 25 1 8.23 -3.23 #> 5 26 1 8.23 -2.21 #> 6 30 1 8.23 -1.18 #> 7 40 1 8.23 -0.318 #> 8 51 1 8.23 -1.10 #> 9 56 1 8.23 -0.448 #> 10 57 1 8.23 -3.80 #> # … with 14,406 more rows #> #> $design #> $design$features #> # A tibble: 12 × 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 #> #> $design$samples #> # A tibble: 3 × 2 #> variable type #> <chr> <chr> #> 1 sampleId sample_primary_key #> 2 name character #> 3 filename character #> #> $design$measurements #> # A tibble: 4 × 2 #> variable type #> <chr> <chr> #> 1 groupId feature_primary_key #> 2 sampleId sample_primary_key #> 3 log2_abundance numeric #> 4 centered_log2_abundance numeric #> #> $design$feature_pk #> [1] "groupId" #> #> $design$sample_pk #> [1] "sampleId" #> #> #> attr(,"class") #> [1] "triple_omic" "tomic" "mzroll"