Convert ADAT to ExpressionSet Object

Utility to convert a SomaLogic soma_adat object to an ExpressionSet object via the Biobase package from Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/Biobase.html.

Usage

adat2eSet(adat)

Arguments

adat: A soma_adat class object as read into the R environment using read_adat().

Value

A Bioconductor object of class ExpressionSet.

Details

The Biobase package is required and must be installed from Bioconductor via the following at the R console:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install("Biobase", version = remotes::bioc_version())

References

https://bioconductor.org/install/

Author

Stu Field

Examples

eSet <- adat2eSet(example_data)
class(eSet)
#> [1] "ExpressionSet"
#> attr(,"package")
#> [1] "Biobase"
eSet
#> ExpressionSet (storageMode: lockedEnvironment)
#> assayData: 5284 features, 192 samples 
#>   element names: exprs 
#> protocolData: none
#> phenoData
#>   sampleNames: 258495800012_3 258495800004_7 ... 258495800110_5
#>     (192 total)
#>   varLabels: PlateId PlateRunDate ... Sex (34 total)
#>   varMetadata: labelDescription
#> featureData
#>   featureNames: seq.10000.28 seq.10001.7 ... seq.9999.1 (5284
#>     total)
#>   fvarLabels: SeqId SeqIdVersion ... Dilution2 (21 total)
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation:  

ft <- Biobase::exprs(eSet)
head(ft[, 1:10L], 10L)
#>               258495800012_3 258495800004_7 258495800010_8 258495800003_4
#> seq.10000.28           476.5          474.4          415.6          442.6
#> seq.10001.7            310.1          293.5          299.6          247.9
#> seq.10003.15           100.3          101.8         3030.1          112.9
#> seq.10006.25           602.8          561.9          563.9          563.7
#> seq.10008.43           561.8          541.9          423.9          469.8
#> seq.10011.65          6897.1         2985.5         3203.6         3140.9
#> seq.10012.5           1796.6         2123.0         2095.6         1922.2
#> seq.10013.34           441.9          521.1          560.4          582.0
#> seq.10014.31           941.7          933.4         1012.0         5207.2
#> seq.10015.119          728.1          477.3          535.1          480.9
#>               258495800009_4 258495800012_8 258495800001_3 258495800004_8
#> seq.10000.28           465.7          496.6          693.0          522.3
#> seq.10001.7            710.7          669.6          614.2          632.8
#> seq.10003.15            95.9          135.5          140.1          101.0
#> seq.10006.25           791.0          826.0          682.7          739.3
#> seq.10008.43           443.5          458.7          481.7          724.7
#> seq.10011.65          2707.5         1705.7         6424.4         3559.6
#> seq.10012.5           1607.1         1396.0         1675.5         1832.8
#> seq.10013.34           438.6          415.7          488.1          483.0
#> seq.10014.31           943.4          801.8          838.9          839.1
#> seq.10015.119          929.2          793.0          454.3          798.0
#>               258495800001_8 258495800004_3
#> seq.10000.28           452.1          702.1
#> seq.10001.7            918.3          237.7
#> seq.10003.15           113.2          126.9
#> seq.10006.25           905.4          634.2
#> seq.10008.43           541.2          585.0
#> seq.10011.65          2674.6         2807.1
#> seq.10012.5           1526.6         1656.6
#> seq.10013.34           747.4          510.6
#> seq.10014.31           815.5          869.1
#> seq.10015.119          981.7          438.9