Node_obj_mRNA_Classifier {bioCancer} | R Documentation |
Atrribute genes expression to color nodes
Node_obj_mRNA_Classifier(geneList,genesclassdetails)
geneList |
A gene list. |
genesclassdetails |
A dataframe with genes classes and genes expression. |
A data frame with node color attributes
r_data <- new.env() input <- NULL r_data[["FreqIn"]] <- structure(list(Genes = c("ATM", "ATR", "BRCA1", "BRCA2", "CHEK1", "CHEK2", "FANCF", "MDC1", "RAD51"), FreqSum = c(0.04, 0.05, 0.05, 0.03, 0.05, 0.04, 0.03, 0.03, 0.02)), .Names = c("Genes", "FreqSum"), class = "data.frame", row.names = c(NA, -9L)) GenesClassDetails <- structure(list(Genes = c("FANCF", "MLH1", "MSH2", "ATR", "PARP1", "CHEK2", "RAD51"), ranking = c(1L, 1L, 1L, 2L, 3L, 1L, 2L), class = c("brca_tcga", "gbm_tcga", "lihc_tcga", "lihc_tcga", "lihc_tcga", "lusc_tcga", "lusc_tcga"), postProb = c(1, 0.99, 1, 0.99, 0.99, 1, 0.98), exprsMeanDiff = c(180, 256, -373, -268, -1482, 258, 143), exprsUpDw = c("UP", "UP", "DOWN", "DOWN", "DOWN", "UP", "UP")), .Names = c("Genes", "ranking", "class", "postProb", "exprsMeanDiff", "exprsUpDw"), class = "data.frame", row.names = c(NA,-7L)) ## Not run: GeneList <- whichGeneList("DNA_damage_Response") nodeObj <- Node_obj_mRNA_Classifier(GeneList, GenesClassDetails) ## End(Not run)