turnPercent {TimiRGeN} | R Documentation |
Genes found in common between the input data and each pathway are normalised by percentages. This is to normalise for pathway size.
turnPercent(MAE, wikiMatrix)
MAE |
MultiAssayExperiment which will store the output from turnPercent. It is recommended to use the MAE which stores output from the wikiMatrix function. |
wikiMatrix |
Numeric matrix of wikipathways and samples. This should be stored as an assay within the MAE used in the wikiMatrix function. |
A percentage matrix which contrasts genes found in pathways and samples. Output will be stored as an assay within the input MAE.
MAE <- MultiAssayExperiment() metadata(MAE)[["e_list"]] <- e_list_mouse metadata(MAE)[["w_list"]] <- w_list_mouse[1:10] MAE <- wikiMatrix(MAE, ID_list = metadata(MAE)[[1]], wp_list = metadata(MAE)[[2]]) MAE <- turnPercent(MAE = MAE, wikiMatrix = assay(MAE, 1))