Node_obj_mRNA_Classifier: Atrribute genes expression to color nodes

In kmezhoud/bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis

Atrribute genes expression to color nodes

Description

Atrribute genes expression to color nodes

Usage

Node_obj_mRNA_Classifier(geneList,genesclassdetails)

Arguments

geneList	A gene list.
genesclassdetails	A dataframe with genes classes and genes expression.

Value

A data frame with node color attributes

Examples

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)

kmezhoud/bioCancer documentation built on Feb. 17, 2024, 10:29 a.m.