Calculate RNA ratios

A helper function calculates the RNA ratios between genes

.RNAratio_calculation(
  gene01 = "EIF4E",
  gene02 = "EIF4E2",
  gene03 = "EIF4E3",
  gene04 = "EIF4EBP1",
  gene05 = "EIF4G1",
  gene06 = "EIF4G2",
  gene07 = "EIF4G3",
  gene08 = "EIF3D",
  gene09 = "EIF4A1",
  gene10 = "EIF4A2"
)

Arguments

gene01

gene name, same input from .plot_boxgraph_RNAratio_TCGA()

gene02

gene name, same input from .plot_boxgraph_RNAratio_TCGA()

gene03

gene name, same input from .plot_boxgraph_RNAratio_TCGA()

gene04

gene name, same input from .plot_boxgraph_RNAratio_TCGA()

gene05

gene name, same input from .plot_boxgraph_RNAratio_TCGA()

gene06

gene name, same input from .plot_boxgraph_RNAratio_TCGA()

gene07

gene name, same input from .plot_boxgraph_RNAratio_TCGA()

gene08

gene name, same input from .plot_boxgraph_RNAratio_TCGA()

gene09

gene name, same input from .plot_boxgraph_RNAratio_TCGA()

gene10

gene name, same input from .plot_boxgraph_RNAratio_TCGA()

Value

a data frame of differential RNA ratios in tumors vs adjacent normal tissues from individual TCGA cancer types

Details

This function

• select the of RNAseq data of input genes from all TCGA samples, using the data frame TCGA_GTEX_RNAseq_sampletype prepared by the function initialize_RNAseq_data().

• calculates the RNA ratio data in each TCGA samples including tumors and solid tissue normal samples for comparison.

It should not be used directly, only inside .plot_boxgraph_RNAratio_TCGA() function.

See also

Other helper function for differential expression analysis: .RNAratio_selection(), .RNAratio_tumortype(), .RNAseq_all_gene(), .RNAseq_ind_gene(), .RNAseq_tumortype()