Transform mae into raw data
Arguments
- mae
MultiAssayExperiment object with SummarizedExperiments containing "RawTreated" and "Controls" assays
Examples
mae <- gDRutils::get_synthetic_data("finalMAE_small")
#> Loading required package: MultiAssayExperiment
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#>
#> Attaching package: ‘MatrixGenerics’
#> The following objects are masked from ‘package:matrixStats’:
#>
#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#> colWeightedMeans, colWeightedMedians, colWeightedSds,
#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#> rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#>
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:stats’:
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#>
#> Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#> as.data.frame, basename, cbind, colnames, dirname, do.call,
#> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
#> tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
#>
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#>
#> findMatches
#> The following objects are masked from ‘package:base’:
#>
#> I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#>
#> Vignettes contain introductory material; view with
#> 'browseVignettes()'. To cite Bioconductor, see
#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
#>
#> Attaching package: ‘Biobase’
#> The following object is masked from ‘package:MatrixGenerics’:
#>
#> rowMedians
#> The following objects are masked from ‘package:matrixStats’:
#>
#> anyMissing, rowMedians
convert_mae_to_raw_data(mae)
#> Loading required package: BumpyMatrix
#> Barcode Concentration masked ReadoutValue Gnumber DrugName drug_moa
#> <char> <num> <lgcl> <num> <char> <char> <char>
#> 1: plate_1 0 FALSE 95.7 vehicle vehicle vehicle
#> 2: plate_1 0 FALSE 100.2 vehicle vehicle vehicle
#> 3: plate_1 0 FALSE 102.6 vehicle vehicle vehicle
#> 4: plate_1 0 FALSE 101.6 vehicle vehicle vehicle
#> 5: plate_1 0 FALSE 99.9 vehicle vehicle vehicle
#> ---
#> 3296: plate_3 10 FALSE 57.7 G00011 drug_011 moa_B
#> 3297: plate_3 10 FALSE 37.7 G00011 drug_011 moa_B
#> 3298: plate_3 10 FALSE 28.6 G00011 drug_011 moa_B
#> 3299: plate_3 10 FALSE 29.6 G00011 drug_011 moa_B
#> 3300: plate_3 10 FALSE 11.0 G00011 drug_011 moa_B
#> Duration clid CellLineName Tissue ReferenceDivisionTime
#> <num> <char> <char> <char> <num>
#> 1: 72 CL00011 cellline_BA tissue_x 26
#> 2: 72 CL00012 cellline_CA tissue_x 30
#> 3: 72 CL00013 cellline_DA tissue_x 34
#> 4: 72 CL00014 cellline_EA tissue_x 38
#> 5: 72 CL00015 cellline_FA tissue_x 42
#> ---
#> 3296: 72 CL00016 cellline_GB tissue_y 46
#> 3297: 72 CL00017 cellline_HB tissue_y 50
#> 3298: 72 CL00018 cellline_IB tissue_y 54
#> 3299: 72 CL00019 cellline_JB tissue_z 58
#> 3300: 72 CL00020 cellline_KB tissue_z 62