CNV ratios in tumors vs adjacent normal tissues across tumor types

Source: R/CNV.R

This function generates boxplot for CNV ratios in tumors vs adjacent normals from individual TCGA cancer types.

.plot_boxgraph_CNVratio_TCGA(gene_list)

Arguments

gene_list

gene names in a vector of characters

Details

This function

  • selects a subset of CNV and sample type data of only EIF4F gene from the data frame TCGA_CNVratio_sampletype - a global variable generated from initialize_cnv_data().

  • uses the subset data .TCGA_CNVratio_sampletype_subset to perform CNV status analysis for each gene across all tumors types with the internal function .CNVratio_tumor() and plots the CNV results with the internal function .CNVratio_boxplot().

This function is not accessible to the user and will not show at the users' workspace. It can only be called by the exported EIF4F_CNV_analysis() function.

Side effects:

(1) the box plots on screen and as saved pdf files to show CNV ratio of gene_list in TCGA tumors vs normals

See also

Other composite function to call CNV data analysis and plotting: .plot_bargraph_CNV_TCGA()

Examples

if (FALSE) {
plot_boxgraph_CNVratio_TCGA(c("EIF4A1", "EIF4E", "EIF4EBP1", "EIF4G1"))
}