normalize_peaks.RdUsing a robust metabolomics normalization rescale ion counts based on the consensus signal of each sample.
Using a sample-level summary, such as number of cells, adjust all values.
Compare each sample to the reference samples within the same batch
Compare each sample to the reference samples within the same batch
normalize_peaks( mzroll_list, normalization_method, quant_peak_varname = "log2_abundance", norm_peak_varname = "normalized_log2_IC", ... ) normalize_peaks_median_polish( mzroll_list, quant_peak_varname, norm_peak_varname, log2_floor_value = NA ) normalize_peaks_loading_value( mzroll_list, quant_peak_varname, norm_peak_varname, loading_varname, log2_floor_value = NA ) normalize_peaks_batch_center( mzroll_list, quant_peak_varname, norm_peak_varname, batch_varnames, log2_floor_value = NA, centering_fxn = mean ) normalize_peaks_reference_sample( mzroll_list, quant_peak_varname, norm_peak_varname, batch_varnames, reference_varname = "sample", reference_values = "posctl", log2_floor_value = NA ) normalize_peaks_reference_condition( mzroll_list, quant_peak_varname, norm_peak_varname, condition_varname = "condition #", reference_varname = "reference condition #", log2_floor_value = NA ) normalize_peaks_loess( mzroll_list, quant_peak_varname, norm_peak_varname, weights_tribble = NULL, log2_floor_value = 12 )
| mzroll_list | output of process_mzroll or process_mzroll_multi
|
|---|---|
| normalization_method | Normalization method to apply
|
| quant_peak_varname | variable in measurements to use for abundance |
| norm_peak_varname | variable in measurements to add for normalized abundance |
| ... | additional arguments to pass to normalization methods |
| log2_floor_value | minimum value to set for low abundance or missing peaks |
| loading_varname | sample variable used for adjustment |
| batch_varnames | variables to use for grouping when removing batch effects |
| centering_fxn | function to use when centering (mean, median, ...) |
| reference_varname | variable specifying which samples are references |
| reference_values | values of |
| condition_varname | variable specifying each sample's condition |
| weights_tribble | a table containing weights and sample variables to match them to. |
a mzroll_list as generated by process_mzroll
a norm_peak_varname variable added to measuremnets
The robust median polish was reported in Kamphorst et al. 2015, see https://github.com/shackett/Pancreatic_tumor_metabolomics.
Note, log2 intensities will be shifted down by this value, so make sure the provided values are appropriately transformed.
reference_varname specifies which condition to contrast a given sample to (using the condition values from condition_varname)
normalize_peaks( nplug_mzroll_augmented, "median polish", quant_peak_varname = "log2_abundance", norm_peak_varname = "normalized_log2_abundance" )#> $features #> # A tibble: 106 × 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 96 more rows, and 5 more variables: searchTableName <chr>, #> # label <chr>, peak_label <chr>, method_tag <chr>, pathway <chr> #> #> $samples #> # A tibble: 136 × 13 #> sampleId name filename samples_tbl_row sample_name month replicate DR #> <fct> <chr> <chr> <int> <chr> <chr> <chr> <dbl> #> 1 1 NH4_0.0… NA 1 NH4_0.055_f… Jun B 0.055 #> 2 2 NH4_0.0… NA 2 NH4_0.055_f… Jun D 0.055 #> 3 3 NH4_0.0… NA 3 NH4_0.055_p… Jun A 0.055 #> 4 4 NH4_0.0… NA 4 NH4_0.055_p… Jun C 0.055 #> 5 5 NH4_0.1… NA 5 NH4_0.173_f… Jun B 0.173 #> 6 6 NH4_0.1… NA 6 NH4_0.173_f… Jun D 0.173 #> 7 7 NH4_0.1… NA 7 NH4_0.173_p… Jun A 0.173 #> 8 8 NH4_0.1… NA 8 NH4_0.173_p… Jun C 0.173 #> 9 9 NH4_0.2… NA 9 NH4_0.210_f… Jun B 0.21 #> 10 10 NH4_0.2… NA 10 NH4_0.210_f… Jun D 0.21 #> # … with 126 more rows, and 5 more variables: limitation <chr>, exp_ref <chr>, #> # extraction <chr>, condition <int>, reference <int> #> #> $measurements #> # A tibble: 14,416 × 5 #> groupId sampleId log2_abundance centered_log2_abundan… normalized_log2_abund… #> <fct> <fct> <dbl> <dbl> <dbl> #> 1 2 1 8.23 -1.27 7.74 #> 2 4 1 8.23 -0.816 7.74 #> 3 15 1 8.23 -4.60 7.74 #> 4 25 1 8.23 -3.23 7.74 #> 5 26 1 8.23 -2.21 7.74 #> 6 30 1 8.23 -1.18 7.74 #> 7 40 1 8.23 -0.318 7.74 #> 8 51 1 8.23 -1.10 7.74 #> 9 56 1 8.23 -0.448 7.74 #> 10 57 1 8.23 -3.80 7.74 #> # … with 14,406 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: 13 × 2 #> variable type #> <chr> <chr> #> 1 sampleId sample_primary_key #> 2 name character #> 3 filename character #> 4 samples_tbl_row integer #> 5 sample_name character #> 6 month character #> 7 replicate character #> 8 DR numeric #> 9 limitation character #> 10 exp_ref character #> 11 extraction character #> 12 condition integer #> 13 reference integer #> #> $design$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"# this examples doesn't make biological sense but its syntactically correct normalize_peaks( nplug_mzroll_augmented, "loading value", quant_peak_varname = "log2_abundance", norm_peak_varname = "normalized_log2_abundance", loading_varname = "DR" )#> $features #> # A tibble: 106 × 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 96 more rows, and 5 more variables: searchTableName <chr>, #> # label <chr>, peak_label <chr>, method_tag <chr>, pathway <chr> #> #> $samples #> # A tibble: 136 × 13 #> sampleId name filename samples_tbl_row sample_name month replicate DR #> <fct> <chr> <chr> <int> <chr> <chr> <chr> <dbl> #> 1 1 NH4_0.0… NA 1 NH4_0.055_f… Jun B 0.055 #> 2 2 NH4_0.0… NA 2 NH4_0.055_f… Jun D 0.055 #> 3 3 NH4_0.0… NA 3 NH4_0.055_p… Jun A 0.055 #> 4 4 NH4_0.0… NA 4 NH4_0.055_p… Jun C 0.055 #> 5 5 NH4_0.1… NA 5 NH4_0.173_f… Jun B 0.173 #> 6 6 NH4_0.1… NA 6 NH4_0.173_f… Jun D 0.173 #> 7 7 NH4_0.1… NA 7 NH4_0.173_p… Jun A 0.173 #> 8 8 NH4_0.1… NA 8 NH4_0.173_p… Jun C 0.173 #> 9 9 NH4_0.2… NA 9 NH4_0.210_f… Jun B 0.21 #> 10 10 NH4_0.2… NA 10 NH4_0.210_f… Jun D 0.21 #> # … with 126 more rows, and 5 more variables: limitation <chr>, exp_ref <chr>, #> # extraction <chr>, condition <int>, reference <int> #> #> $measurements #> # A tibble: 14,416 × 5 #> groupId sampleId log2_abundance centered_log2_abundan… normalized_log2_abund… #> <fct> <fct> <dbl> <dbl> <dbl> #> 1 2 1 8.23 -1.27 8.17 #> 2 4 1 8.23 -0.816 8.17 #> 3 15 1 8.23 -4.60 8.17 #> 4 25 1 8.23 -3.23 8.17 #> 5 26 1 8.23 -2.21 8.17 #> 6 30 1 8.23 -1.18 8.17 #> 7 40 1 8.23 -0.318 8.17 #> 8 51 1 8.23 -1.10 8.17 #> 9 56 1 8.23 -0.448 8.17 #> 10 57 1 8.23 -3.80 8.17 #> # … with 14,406 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: 13 × 2 #> variable type #> <chr> <chr> #> 1 sampleId sample_primary_key #> 2 name character #> 3 filename character #> 4 samples_tbl_row integer #> 5 sample_name character #> 6 month character #> 7 replicate character #> 8 DR numeric #> 9 limitation character #> 10 exp_ref character #> 11 extraction character #> 12 condition integer #> 13 reference integer #> #> $design$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"normalize_peaks( nplug_mzroll_augmented, "center batches", quant_peak_varname = "log2_abundance", norm_peak_varname = "normalized_log2_abundance", batch_varnames = "month", centering_fxn = median )#> $features #> # A tibble: 106 × 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 96 more rows, and 5 more variables: searchTableName <chr>, #> # label <chr>, peak_label <chr>, method_tag <chr>, pathway <chr> #> #> $samples #> # A tibble: 136 × 13 #> sampleId name filename samples_tbl_row sample_name month replicate DR #> <fct> <chr> <chr> <int> <chr> <chr> <chr> <dbl> #> 1 1 NH4_0.0… NA 1 NH4_0.055_f… Jun B 0.055 #> 2 2 NH4_0.0… NA 2 NH4_0.055_f… Jun D 0.055 #> 3 3 NH4_0.0… NA 3 NH4_0.055_p… Jun A 0.055 #> 4 4 NH4_0.0… NA 4 NH4_0.055_p… Jun C 0.055 #> 5 5 NH4_0.1… NA 5 NH4_0.173_f… Jun B 0.173 #> 6 6 NH4_0.1… NA 6 NH4_0.173_f… Jun D 0.173 #> 7 7 NH4_0.1… NA 7 NH4_0.173_p… Jun A 0.173 #> 8 8 NH4_0.1… NA 8 NH4_0.173_p… Jun C 0.173 #> 9 9 NH4_0.2… NA 9 NH4_0.210_f… Jun B 0.21 #> 10 10 NH4_0.2… NA 10 NH4_0.210_f… Jun D 0.21 #> # … with 126 more rows, and 5 more variables: limitation <chr>, exp_ref <chr>, #> # extraction <chr>, condition <int>, reference <int> #> #> $measurements #> # A tibble: 14,416 × 5 #> groupId sampleId log2_abundance centered_log2_abundan… normalized_log2_abund… #> <fct> <fct> <dbl> <dbl> <dbl> #> 1 2 1 8.23 -1.27 8.23 #> 2 4 1 8.23 -0.816 8.23 #> 3 15 1 8.23 -4.60 8.30 #> 4 25 1 8.23 -3.23 9.69 #> 5 26 1 8.23 -2.21 9.14 #> 6 30 1 8.23 -1.18 8.23 #> 7 40 1 8.23 -0.318 8.23 #> 8 51 1 8.23 -1.10 8.47 #> 9 56 1 8.23 -0.448 8.23 #> 10 57 1 8.23 -3.80 8.64 #> # … with 14,406 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: 13 × 2 #> variable type #> <chr> <chr> #> 1 sampleId sample_primary_key #> 2 name character #> 3 filename character #> 4 samples_tbl_row integer #> 5 sample_name character #> 6 month character #> 7 replicate character #> 8 DR numeric #> 9 limitation character #> 10 exp_ref character #> 11 extraction character #> 12 condition integer #> 13 reference integer #> #> $design$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"normalize_peaks( nplug_mzroll_augmented, normalization_method = "reference condition", quant_peak_varname = "log2_abundance", norm_peak_varname = "normalized_log2_abundance", condition_varname = "condition", reference_varname = "reference" )#> $features #> # A tibble: 106 × 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 96 more rows, and 5 more variables: searchTableName <chr>, #> # label <chr>, peak_label <chr>, method_tag <chr>, pathway <chr> #> #> $samples #> # A tibble: 136 × 13 #> sampleId name filename samples_tbl_row sample_name month replicate DR #> <fct> <chr> <chr> <int> <chr> <chr> <chr> <dbl> #> 1 1 NH4_0.0… NA 1 NH4_0.055_f… Jun B 0.055 #> 2 2 NH4_0.0… NA 2 NH4_0.055_f… Jun D 0.055 #> 3 3 NH4_0.0… NA 3 NH4_0.055_p… Jun A 0.055 #> 4 4 NH4_0.0… NA 4 NH4_0.055_p… Jun C 0.055 #> 5 5 NH4_0.1… NA 5 NH4_0.173_f… Jun B 0.173 #> 6 6 NH4_0.1… NA 6 NH4_0.173_f… Jun D 0.173 #> 7 7 NH4_0.1… NA 7 NH4_0.173_p… Jun A 0.173 #> 8 8 NH4_0.1… NA 8 NH4_0.173_p… Jun C 0.173 #> 9 9 NH4_0.2… NA 9 NH4_0.210_f… Jun B 0.21 #> 10 10 NH4_0.2… NA 10 NH4_0.210_f… Jun D 0.21 #> # … with 126 more rows, and 5 more variables: limitation <chr>, exp_ref <chr>, #> # extraction <chr>, condition <int>, reference <int> #> #> $measurements #> # A tibble: 14,416 × 5 #> groupId sampleId log2_abundance centered_log2_abundan… normalized_log2_abund… #> <fct> <fct> <dbl> <dbl> <dbl> #> 1 2 1 8.23 -1.27 0 #> 2 4 1 8.23 -0.816 -2.00 #> 3 15 1 8.23 -4.60 -5.72 #> 4 25 1 8.23 -3.23 -7.23 #> 5 26 1 8.23 -2.21 -5.16 #> 6 30 1 8.23 -1.18 -3.68 #> 7 40 1 8.23 -0.318 -0.200 #> 8 51 1 8.23 -1.10 -3.93 #> 9 56 1 8.23 -0.448 -2.45 #> 10 57 1 8.23 -3.80 -10.1 #> # … with 14,406 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: 13 × 2 #> variable type #> <chr> <chr> #> 1 sampleId sample_primary_key #> 2 name character #> 3 filename character #> 4 samples_tbl_row integer #> 5 sample_name character #> 6 month character #> 7 replicate character #> 8 DR numeric #> 9 limitation character #> 10 exp_ref character #> 11 extraction character #> 12 condition integer #> 13 reference integer #> #> $design$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"normalize_peaks( nplug_mzroll_augmented, normalization_method = "reference sample", quant_peak_varname = "log2_abundance", norm_peak_varname = "normalized_log2_abundance", batch_varnames = c("month", "extraction"), reference_varname = "exp_ref", reference_values = "ref" )#> $features #> # A tibble: 106 × 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 96 more rows, and 5 more variables: searchTableName <chr>, #> # label <chr>, peak_label <chr>, method_tag <chr>, pathway <chr> #> #> $samples #> # A tibble: 136 × 13 #> sampleId name filename samples_tbl_row sample_name month replicate DR #> <fct> <chr> <chr> <int> <chr> <chr> <chr> <dbl> #> 1 1 NH4_0.0… NA 1 NH4_0.055_f… Jun B 0.055 #> 2 2 NH4_0.0… NA 2 NH4_0.055_f… Jun D 0.055 #> 3 3 NH4_0.0… NA 3 NH4_0.055_p… Jun A 0.055 #> 4 4 NH4_0.0… NA 4 NH4_0.055_p… Jun C 0.055 #> 5 5 NH4_0.1… NA 5 NH4_0.173_f… Jun B 0.173 #> 6 6 NH4_0.1… NA 6 NH4_0.173_f… Jun D 0.173 #> 7 7 NH4_0.1… NA 7 NH4_0.173_p… Jun A 0.173 #> 8 8 NH4_0.1… NA 8 NH4_0.173_p… Jun C 0.173 #> 9 9 NH4_0.2… NA 9 NH4_0.210_f… Jun B 0.21 #> 10 10 NH4_0.2… NA 10 NH4_0.210_f… Jun D 0.21 #> # … with 126 more rows, and 5 more variables: limitation <chr>, exp_ref <chr>, #> # extraction <chr>, condition <int>, reference <int> #> #> $measurements #> # A tibble: 14,416 × 5 #> groupId sampleId log2_abundance centered_log2_abundan… normalized_log2_abund… #> <fct> <fct> <dbl> <dbl> <dbl> #> 1 2 1 8.23 -1.27 0 #> 2 4 1 8.23 -0.816 -2.00 #> 3 15 1 8.23 -4.60 -5.72 #> 4 25 1 8.23 -3.23 -7.23 #> 5 26 1 8.23 -2.21 -5.16 #> 6 30 1 8.23 -1.18 -3.68 #> 7 40 1 8.23 -0.318 -0.200 #> 8 51 1 8.23 -1.10 -3.93 #> 9 56 1 8.23 -0.448 -2.45 #> 10 57 1 8.23 -3.80 -10.1 #> # … with 14,406 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: 13 × 2 #> variable type #> <chr> <chr> #> 1 sampleId sample_primary_key #> 2 name character #> 3 filename character #> 4 samples_tbl_row integer #> 5 sample_name character #> 6 month character #> 7 replicate character #> 8 DR numeric #> 9 limitation character #> 10 exp_ref character #> 11 extraction character #> 12 condition integer #> 13 reference integer #> #> $design$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"