Define assay names

Starting from a base assay name and a few decisions about the workflow, define the names of assays that will be generated in the einprot workflow and included in the final SingleCellExperiment object.

defineAssayNames(aName, normMethod, doBatchCorr)

Arguments

aName

Base assay name, typically obtained from importExperiment.

normMethod

Character scalar, indicating the normalization method. See doNormalization for available options. Set to "none" if no between-sample normalization will be performed.

doBatchCorr

Logical scalar indicating whether or not batch correction will be performed.

Value

A list with assay names that will be used for assays created at different steps in the einprot workflows.

Author

Charlotte Soneson

Examples

sce <- importExperiment(system.file("extdata", "mq_example",
                                    "1356_proteinGroups.txt",
                                    package = "einprot"),
                        iColPattern = "^iBAQ\\.")
defineAssayNames(sce$aName, normMethod = "none", doBatchCorr = FALSE)
#> $assayInput
#> [1] "iBAQ"
#> 
#> $assayLog2WithNA
#> [1] "log2_iBAQ_withNA"
#> 
#> $assayImputIndic
#> [1] "imputed_iBAQ"
#> 
#> $assayLog2NormWithNA
#> [1] "log2_iBAQ_withNA"
#> 
#> $assayImputed
#> [1] "log2_iBAQ"
#> 
#> $assayBatchCorr
#> [1] "log2_iBAQ"
#>