dot-RNAratio_calculation: Calculate RNA ratios

In a3609640/eIF4F.analysis: A R package to analyze eIF4F subunits in human cancers

Calculate RNA ratios

Description

A helper function calculates the RNA ratios between genes

Usage

.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()

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.

Value

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

See Also

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

a3609640/eIF4F.analysis documentation built on Jan. 2, 2023, 11:19 p.m.