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library(metaboprep)

# Somalogic data file path
filepath <- system.file("extdata", "somalogic_v1_example.adat", package = "metaboprep")

# read Somalogic data
somalogic_data <- read_somalogic(filepath)

# create the object (downsampled for speed)
m <- Metaboprep(data     = somalogic_data$data[1:9, 1:100], 
                samples  = somalogic_data$samples[1:9, ], 
                features = somalogic_data$features[1:100, ])

# run QC
m <- m |>
  quality_control(source_layer = "input", 
                  sample_missingness  = 0.5, 
                  feature_missingness = 0.3, 
                  total_peak_area_sd  = 5, 
                  outlier_udist       = 5, 
                  outlier_treatment   = "leave_be", 
                  winsorize_quantile  = 1.0, 
                  tree_cut_height     = 0.5, 
                  pc_outlier_sd       = 5, 
                  sample_ids          = NULL, 
                  feature_ids         = NULL)
#> 
#> ── Starting Metabolite QC Process ──────────────────────────────────────────────
#>  Validating input parameters
#>  Validating input parameters [9ms]
#> 
#>  Sample & Feature Summary Statistics for raw data
#>  Sample & Feature Summary Statistics for raw data [471ms]
#> 
#>  Copying input data to new 'qc' data layer
#>  Copying input data to new 'qc' data layer [24ms]
#> 
#>  Assessing for extreme sample missingness >=80% - excluding 0 sample(s)
#>  Assessing for extreme sample missingness >=80% - excluding 0 sample(s) [18ms]
#> 
#>  Assessing for extreme feature missingness >=80% - excluding 0 feature(s)
#>  Assessing for extreme feature missingness >=80% - excluding 0 feature(s) [18m
#> 
#>  Assessing for sample missingness at specified level of >=50% - excluding 0 sa…
#>  Assessing for sample missingness at specified level of >=50% - excluding 0 sa…
#> 
#>  Assessing for feature missingness at specified level of >=30% - excluding 0 f…
#>  Assessing for feature missingness at specified level of >=30% - excluding 0 f…
#> 
#>  Calculating total peak abundance outliers at +/- 5 Sdev - excluding 0 sample(…
#>  Calculating total peak abundance outliers at +/- 5 Sdev - excluding 0 sample(…
#> 
#>  Running sample data PCA outlier analysis at +/- 5 Sdev
#>  Running sample data PCA outlier analysis at +/- 5 Sdev [18ms]
#> 
#>  Sample PCA outlier analysis - re-identify feature independence and PC outlier…
#>  Sample PCA outlier analysis - re-identify feature independence and PC outlier…
#>  Sample PCA outlier analysis - re-identify feature independence and PC outlier…
#> 
#>  Creating final QC dataset...
#>  Creating final QC dataset... [422ms]
#> 
#>  Metabolite QC Process Completed
#>  Metabolite QC Process Completed [16ms]
#>