genMissingOmics {MultiBaC} | R Documentation |
This function generates for all the batches the omic data they had not originally. This is the previous step to apply ARSyNbac [1] correction.
genMissingOmics(mbac)
mbac |
mbac object generated by *createMbac*. PLS models slot must be present. |
A list of *MultiAssayExperiment* structures. In this case, each batch contains all the omics introduced in MultiBaC. For instance, if two batches are being studying, "A" and "B", given that "A" contains "RNA-seq" and "GRO-seq" data and "B" contains "RNA-seq" and "Metabolomica" data, after applying *genMissingOmics* function batch "A" will contain "RNA-seq", "GRO-seq" and predicted "Metabolomics" data.
data('multiyeast') my_mbac <- createMbac (inputOmics = list(A.rna, A.gro, B.rna, B.ribo, C.rna, C.par), batchFactor = c("A", "A", "B", "B", "C", "C"), experimentalDesign = list("A" = c("Glu+", "Glu+", "Glu+", "Glu-", "Glu-", "Glu-"), "B" = c("Glu+", "Glu+", "Glu-", "Glu-"), "C" = c("Glu+", "Glu+", "Glu-", "Glu-")), omicNames = c("RNA", "GRO", "RNA", "RIBO", "RNA", "PAR"), commonOmic = "RNA") my_mbac_2 <- genModelList (my_mbac, test.comp = NULL, scale = FALSE, center = TRUE, crossval = NULL, showinfo = TRUE) multiBatchDesign <- genMissingOmics(my_mbac_2)