library(omiprep)
# import data
m <- read_metabolon(system.file("extdata", "metabolon_v1.1_example.xlsx", package = "omiprep"),
sheet = "OrigScale", ## The name of the sheet in the excel file to read in
return_Omiprep = TRUE ## Whether to return a Omiprep object (TRUE) or a list (FALSE)
)
Run the quality control pipeline
# run QC
m <- quality_control(m,
source_layer = "input",
sample_missingness = 0.2,
feature_missingness = 0.2,
feature_skewness_threshold = NULL,
feature_skewness_direction = "left",
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,
cores = 1)
#>
#> ── Starting Omics QC Process ───────────────────────────────────────────────────
#> ℹ Validating input parameters
#>
#> ℹ Validating input parameters── Starting 'Omics QC Process ──────────────────────────────────────────────────
#> ℹ Validating input parameters✔ Validating input parameters [17ms]
#>
#> ℹ Validating input parameters
#> ✔ Validating input parameters [13ms]
#>
#> ℹ Sample & Feature Summary Statistics for raw data
#> AF = 2
#> ✔ Sample & Feature Summary Statistics for raw data [561ms]
#>
#> ℹ Copying input data to new 'qc' data layer
#> ✔ Copying input data to new 'qc' data layer [23ms]
#>
#> ℹ Assessing for extreme sample missingness >=80% - excluding 0 sample(s)
#> ✔ Assessing for extreme sample missingness >=80% - excluding 0 sample(s) [24ms]
#>
#> ℹ Assessing for extreme feature missingness >=80% - excluding 0 feature(s)
#> ✔ Assessing for extreme feature missingness >=80% - excluding 0 feature(s) [16m…
#>
#> ℹ Assessing for sample missingness at specified level of >=20% - excluding 0 sa…
#> ✔ Assessing for sample missingness at specified level of >=20% - excluding 2 sa…
#>
#> ℹ Assessing for feature missingness at specified level of >=20% - excluding 0 f…
#> ✔ Assessing for feature missingness at specified level of >=20% - excluding 0 f…
#>
#> ℹ Calculating total peak abundance outliers at +/- 5 Sdev - excluding 0 sample(…
#> ✔ Calculating total peak abundance outliers at +/- 5 Sdev - excluding 0 sample(…
#>
#> ℹ Running sample data PCA outlier analysis at +/- 5 Sdev
#> ✔ Running sample data PCA outlier analysis at +/- 5 Sdev [24ms]
#>
#> ℹ Sample PCA outlier analysis - re-identify feature independence and PC outlier…
#> AF = 2
#> ! The stated max PCs [max_num_pcs=10] to use in PCA outlier assessment is greater than the number of available informative PCs [2]
#> ℹ Sample PCA outlier analysis - re-identify feature independence and PC outlier…✔ Sample PCA outlier analysis - re-identify feature independence and PC outlier…
#>
#> ℹ Creating final QC dataset...
#> AF = 2
#>
#> ℹ Creating final QC dataset...── Step timings ──
#> ℹ Creating final QC dataset...
#> ℹ Creating final QC dataset...
#> step seconds pct
#> validation 0.02 1.0
#> summarise_raw 0.54 28.0
#> copy_layer 0.00 0.0
#> extreme_sample_missingness 0.00 0.0
#> extreme_feature_missingness 0.00 0.0
#> sample_missingness 0.00 0.0
#> total_peak_area 0.00 0.0
#> summarise_pca 0.61 31.7
#> summarise_final 0.53 27.5
#> total 1.93 100.2
#> ✔ Creating final QC dataset... [570ms]
#>
#> ℹ 'Omics QC Process Completed
#> ✔ 'Omics QC Process Completed [23ms]
View a summary of the Omiprep object
# view summary
summary(m)
#> Omiprep Object Summary
#> --------------------------
#> Samples : 100
#> Features : 100
#> Data Layers : 2
#> Layer Names : input, qc
#>
#> Sample Summary Layers : input, qc
#> Feature Summary Layers: input, qc
#>
#> Sample Annotation (metadata):
#> Columns: 8
#> Names : sample_id, neg, pos, run_day, box_id, lot, reason_excluded, excluded
#>
#> Feature Annotation (metadata):
#> Columns: 9
#> Names : feature_id, metabolite_id, comp_id, platform, pathway, kegg, group_hmdb, reason_excluded, excluded
#>
#> Exclusion Codes Summary:
#>
#> Sample Exclusions:
#> Exclusion | Count
#> -----------------
#> user_excluded | 0
#> extreme_sample_missingness | 0
#> user_defined_sample_missingness | 2
#> user_defined_sample_totalpeakarea | 0
#> user_defined_sample_pca_outlier | 0
#>
#> Feature Exclusions:
#> Exclusion | Count
#> -----------------
#> user_excluded | 0
#> extreme_feature_missingness | 0
#> user_defined_feature_missingness | 0
#> user_defined_feature_skewness | 0
