readAdat: Read a SomaLogic data file
In readat: Functionality to Read and Manipulate SomaLogic ADAT files

Description Usage Arguments Value Author(s) Examples

Reads a SomaLogic ADAT data file.

1 2	readAdat(file, keepOnlyPasses = TRUE, keepOnlySamples = TRUE, dateFormat = "%Y-%m-%d", verbose = getOption("verbose"))

`file`	A string containing the path to the file to be read.
`keepOnlyPasses`	A logical value indicating whether or not to keep only the rows and columns where the data quality was considered to be passable.
`keepOnlySamples`	A logical value indicating whether or not to keep only the rows containing actual samples (as opposed to QC, buffer, and calibrator samples).
`dateFormat`	A string describing the format of the dates contained in the file's metadata. See `strptime` for how to specify these.
`verbose`	Logical value indicating whether (lots of) diagnostic messages should be shown.

An object of class WideSomaLogicData, which inherits from data.table. The return value consists of a data frame where each row represents a sample. Initial columns contain sample metadata and later columns contain intensities of proteins. The specific metadata columns are not fixed, but the most useful ones described below should always be present.

SampleUniqueID: A unique identifier for the sample.
Subject_ID: A unique identifier for the person being sampled.
RowCheck: This should have the value "PASS" if the data quality is acceptable.

Columns of proteins intensities have a name beginning SeqId.. Return value also has three attributes.

SequenceData: A data frame.
Metadata: A list of experimental metadata values.
Checksum: A SHA1 checksum to ensure file integrity.

Richard Cotton

somaFile <- extractSampleData()
wideSomaData <- readAdat(somaFile)
str(wideSomaData, list.len = 35)
unlink(somaFile)

Removing 11 sequences that failed QC.
Classes 'WideSomaLogicData', 'data.table' and 'data.frame':	20 obs. of  1326 variables:
 $ PlateId            : Factor w/ 1 level "Set 01": 1 1 1 1 1 1 1 1 1 1 ...
 $ ScannerID          : Factor w/ 1 level "SG12344217": 1 1 1 1 1 1 1 1 1 1 ...
 $ PlatePosition      : Factor w/ 20 levels "A5","A6","B1",..: 19 14 9 12 15 8 1 20 7 2 ...
 $ SlideId            : Factor w/ 12 levels "257711010447",..: 8 5 3 7 9 12 6 9 2 7 ...
 $ Subarray           : int  8 6 4 5 6 4 1 8 4 1 ...
 $ SampleId           : Factor w/ 20 levels "1029","1050",..: 20 14 18 4 1 3 5 11 7 8 ...
 $ SampleType         : Factor w/ 1 level "Sample": 1 1 1 1 1 1 1 1 1 1 ...
 $ PercentDilution    : int  40 40 40 40 40 40 40 40 40 40 ...
 $ SampleMatrix       : Factor w/ 1 level "Plasma": 1 1 1 1 1 1 1 1 1 1 ...
 $ Barcode            : Factor w/ 20 levels "S622008","S622032",..: 20 14 18 4 1 3 5 11 7 8 ...
 $ Barcode2d          : Factor w/ 20 levels "0188777585","0188777599",..: 2 6 1 16 8 18 11 15 19 10 ...
 $ SampleNotes        : Factor w/ 0 levels: NA NA NA NA NA NA NA NA NA NA ...
 $ SampleDescription  : Factor w/ 0 levels: NA NA NA NA NA NA NA NA NA NA ...
 $ AssayNotes         : Factor w/ 0 levels: NA NA NA NA NA NA NA NA NA NA ...
 $ TimePoint          : Factor w/ 2 levels "Old","Young": 2 2 2 2 2 2 2 2 2 2 ...
 $ ExtIdentifier      : Factor w/ 20 levels "EXID19881435244840",..: 1 2 3 4 5 6 7 8 9 10 ...
 $ SsfExtId           : Factor w/ 20 levels "109863","109864",..: 15 11 9 2 17 1 12 18 8 13 ...
 $ SampleGroup        : Factor w/ 2 levels "F","M": 1 1 1 1 1 2 2 2 2 2 ...
 $ SiteId             : Factor w/ 1 level "Covance": 1 1 1 1 1 1 1 1 1 1 ...
 $ TubeUniqueID       : Factor w/ 5 levels "1113.0","1132.0",..: NA NA NA 2 NA 1 NA NA NA NA ...
 $ Subject_ID         : Factor w/ 20 levels "1029","1050",..: 20 14 18 4 1 3 5 11 7 8 ...
 $ SampleUniqueID     : int  4178 3104 4140 1133 1029 1113 1149 2264 2158 2159 ...
 $ HybControlNormScale: num  0.646 0.644 0.619 0.664 0.689 0.693 0.664 0.703 0.665 0.648 ...
 $ RowCheck           : Factor w/ 1 level "PASS": 1 1 1 1 1 1 1 1 1 1 ...
 $ NormScale_1        : num  1.097 0.998 1.142 0.906 1.026 ...
 $ NormScale_40       : num  1.096 1.007 1.146 0.856 0.997 ...
 $ NormScale_0_005    : num  0.978 1.014 0.988 1.047 1.065 ...
 $ SeqId.10336-3_3    : num  730 3607 612 3381 4288 ...
 $ SeqId.10337-83_3   : num  2367 669 715 706 969 ...
 $ SeqId.10339-48_3   : num  37373 31239 15778 28725 60925 ...
 $ SeqId.10342-55_3   : num  2442 595 849 671 540 ...
 $ SeqId.10344-334_3  : num  1343 1067 1227 1062 1222 ...
 $ SeqId.10346-5_3    : num  627 2860 951 5395 3565 ...
 $ SeqId.10351-51_3   : num  1453 1663 1081 2053 1836 ...
 $ SeqId.10356-21_3   : num  5748 1501 1668 1404 1359 ...
  [list output truncated]
 - attr(*, ".internal.selfref")=<externalptr> 
 - attr(*, "sorted")= chr "ExtIdentifier"
 - attr(*, "SequenceData")=Classes 'data.table' and 'data.frame':	1299 obs. of  14 variables:
  ..$ SeqId           : Factor w/ 1310 levels "10336-3_3","10337-83_3",..: 1 2 3 4 5 6 7 8 9 10 ...
  ..$ SomaId          : Factor w/ 1310 levels "SL000001","SL000002",..: 1305 888 231 1304 721 899 885 126 414 1250 ...
  ..$ TargetFullName  : Factor w/ 1310 levels "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1",..: 390 186 506 389 659 1120 649 1176 611 9 ...
  ..$ Target          : Factor w/ 1310 levels "14-3-3","14-3-3 protein beta/alpha",..: 201 199 859 937 599 1090 663 1255 819 875 ...
  ..$ UniProt         : Factor w/ 1277 levels "O00170","O00175",..: 1249 478 350 1037 918 665 396 274 878 148 ...
  ..$ EntrezGeneID    : Factor w/ 1267 levels "1000","100049587",..: 22 35 210 707 507 975 528 535 598 660 ...
  ..$ EntrezGeneSymbol: Factor w/ 1274 levels "A2M","ABL1","ABL2",..: 1146 228 393 940 618 1140 686 698 802 889 ...
  ..$ Organism        : Factor w/ 5 levels "Human","Human papillomavirus type 16",..: 1 1 1 1 1 1 1 1 1 1 ...
  ..$ Units           : Factor w/ 1 level "RFU": 1 1 1 1 1 1 1 1 1 1 ...
  ..$ Type            : chr  "Protein" "Protein" "Protein" "Protein" ...
  ..$ Dilution        : num  40 40 40 40 1 1 40 40 40 40 ...
  ..$ CalReference    : num  1090 566 14324 555 924 ...
  ..$ Cal_Set_01      : num  1.152 0.986 1.151 0.937 1 ...
  ..$ ColCheck        : Factor w/ 2 levels "PASS","FLAG": 1 1 1 1 1 1 1 1 1 1 ...
  ..- attr(*, ".internal.selfref")=<externalptr> 
  ..- attr(*, "sorted")= chr "SeqId"
 - attr(*, "Metadata")=List of 23
  ..$ Version                :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. ..$ : int  1 2
  ..$ AssayType              : chr "PharmaServices"
  ..$ AssayVersion           : chr "V3.2"
  ..$ AssayRobot             : chr "TECAN 1"
  ..$ CreatedBy              : chr "PharmaServices"
  ..$ CreatedDate            : Date, format: "2015-10-30"
  ..$ EnteredBy              : chr "DP"
  ..$ ExpDate                : Date, format: "2015-10-30"
  ..$ GeneratedBy            : chr "Px (Build: 947 : c849b20284affe7c7e19f21c575f44fcc2a6a8f7)"
  ..$ MasterMixVersion       : chr "1.3k Plasma"
  ..$ ProcessSteps           : chr "Raw RFU, Hyb Normalization, Median Normalization([SampleType]), Calibration, Filtered"
  ..$ ProteinEffectiveDate   : Date, format: "2015-10-30"
  ..$ StudyMatrix            : chr "EDTA Plasma"
  ..$ StudyOrganism          : chr "Human"
  ..$ Title                  : chr "QC-15-166"
  ..$ HybNormReference       : chr "HybridizationReference.8n.SL19239.amid2538564.20150821"
  ..$ CalibrationReference   : chr "EDTAplasma_Tec_Cal_SL16485_9o_1.3k_mm3.3_p3.2"
  ..$ PlateMedianCal_Set_01  : num 1.06
  ..$ PlateMedianTest_Set_01 : chr "PASS"
  ..$ PlateTailPercent_Set_01: num 0.9
  ..$ PlateTailTest_Set_01   : chr "PASS"
  ..$ SomascanMenuVersion    : chr "1.3k"
  ..$ FilteringOptions       : chr "somascanMenuVersion + 1.3k, filteredMetadata + Notes, RunNotes"
 - attr(*, "Checksum")= chr "2a8c4ae17f390f3b2d0ba3af43fc75f4bc9fff27"