Import Somalogic Proteomic Data
somalogic.RmdImport SomaLogic data
Read in the SomaLogic data using the read_somalogic
function. Here we will read in the example data provided with the
package, as a list object.
library(omiprep)
# example file
filepath <- system.file("extdata", "somalogic_v1_example.adat", package = "omiprep")
# import
dat <- read_somalogic(filepath,
return_Omiprep = FALSE)
# create the object (down-sampled for speed)
m <- Omiprep(data = dat$data[1:9, 1:100],
samples = dat$samples[1:9, ],
features = dat$features[1:100, ]
)Quick look to identify the types of data imported
Note that we would advocate that you read in olink data as a list
object first, as it will often have additional information that you may
wish to inspect prior to creating the Omiprep object.
names(dat)
#> [1] "data" "samples" "features" "controls"
#> [5] "control_metadata"Create Omiprep object
Once imported, we pass the data to the Omiprep() function to build
the Omiprep class object.
mydata <- Omiprep(data = dat$data[1:9, 1:100],
samples = dat$samples[1:9, ],
features = dat$features[1:100, ]
)Quick summary of the Omiprep object
summary(mydata)
#> Omiprep Object Summary
#> --------------------------
#> Samples : 9
#> Features : 100
#> Data Layers : 1
#> Layer Names : input
#>
#> Sample Summary Layers : none
#> Feature Summary Layers: none
#>
#> Sample Annotation (metadata):
#> Columns: 34
#> Names : sample_id, PlateId, PlateRunDate, ScannerID, PlatePosition, SlideId, Subarray, SampleType, PercentDilution, SampleMatrix, Barcode, Barcode2d, SampleName, SampleNotes, AliquotingNotes, SampleDescription, AssayNotes, TimePoint, ExtIdentifier, SsfExtId, SampleGroup, SiteId, TubeUniqueID, CLI, HybControlNormScale, RowCheck, NormScale_20, NormScale_0_005, NormScale_0_5, ANMLFractionUsed_20, ANMLFractionUsed_0_005, ANMLFractionUsed_0_5, Age, Sex
#>
#> Feature Annotation (metadata):
#> Columns: 22
#> Names : feature_id, SeqId, SeqIdVersion, SomaId, TargetFullName, Target, UniProt, EntrezGeneID, EntrezGeneSymbol, Organism, Units, Type, Dilution, PlateScale_Reference, CalReference, Cal_Example_Adat_Set001, ColCheck, CalQcRatio_Example_Adat_Set001_170255, QcReference_170255, Cal_Example_Adat_Set002, CalQcRatio_Example_Adat_Set002_170255, Dilution2
#>
#> Exclusion Codes Summary:
#>
#> Sample Exclusions:
#> Exclusion | Count
#> -----------------
#> user_excluded | 0
#> extreme_sample_missingness | 0
#> user_defined_sample_missingness | 0
#> 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 | 0QC Olink data
Perform the QC steps using the quality_control
function.
mydata <- mydata |>
quality_control(source_layer = "input",
sample_missingness = 0.2,
feature_missingness = 0.2,
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,
feature_selection = "max_var_exp",
features_exclude_but_keep = 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 [18ms]
#>
#> ℹ Validating input parameters
#> ✔ Validating input parameters [14ms]
#>
#> ℹ Sample & Feature Summary Statistics for raw data
#> AF = 1
#> ✔ Sample & Feature Summary Statistics for raw data [389ms]
#>
#> 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) [16ms]
#>
#> 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 0 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 [17ms]
#>
#> ℹ Sample PCA outlier analysis - re-identify feature independence and PC outlier…
#> AF = 1
#> ! 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 = 1
#>
#> ℹ Creating final QC dataset...── Step timings ──
#> ℹ Creating final QC dataset...
#> ℹ Creating final QC dataset...
#> step seconds pct
#> validation 0.02 1.5
#> summarise_raw 0.37 27.8
#> 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 0.43 32.3
#> summarise_final 0.32 24.0
#> total 1.33 99.8
#> ✔ Creating final QC dataset... [347ms]
#>
#> ℹ 'Omics QC Process Completed
#> ✔ 'Omics QC Process Completed [14ms]Quick summary of the Omiprep object following QC
summary(mydata)
#> Omiprep Object Summary
#> --------------------------
#> Samples : 9
#> Features : 100
#> Data Layers : 2
#> Layer Names : input, qc
#>
#> Sample Summary Layers : input, qc
#> Feature Summary Layers: input, qc
#>
#> Sample Annotation (metadata):
#> Columns: 36
#> Names : sample_id, PlateId, PlateRunDate, ScannerID, PlatePosition, SlideId, Subarray, SampleType, PercentDilution, SampleMatrix, Barcode, Barcode2d, SampleName, SampleNotes, AliquotingNotes, SampleDescription, AssayNotes, TimePoint, ExtIdentifier, SsfExtId, SampleGroup, SiteId, TubeUniqueID, CLI, HybControlNormScale, RowCheck, NormScale_20, NormScale_0_005, NormScale_0_5, ANMLFractionUsed_20, ANMLFractionUsed_0_005, ANMLFractionUsed_0_5, Age, Sex, reason_excluded, excluded
#>
#> Feature Annotation (metadata):
#> Columns: 24
#> Names : feature_id, SeqId, SeqIdVersion, SomaId, TargetFullName, Target, UniProt, EntrezGeneID, EntrezGeneSymbol, Organism, Units, Type, Dilution, PlateScale_Reference, CalReference, Cal_Example_Adat_Set001, ColCheck, CalQcRatio_Example_Adat_Set001_170255, QcReference_170255, Cal_Example_Adat_Set002, CalQcRatio_Example_Adat_Set002_170255, Dilution2, reason_excluded, excluded
#>
#> Exclusion Codes Summary:
#>
#> Sample Exclusions:
#> Exclusion | Count
#> -----------------
#> user_excluded | 0
#> extreme_sample_missingness | 0
#> user_defined_sample_missingness | 0
#> 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