dot-plot_boxgraph_CNVratio_TCGA: CNV ratios in tumors vs adjacent normal tissues across tumor...

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

CNV ratios in tumors vs adjacent normal tissues across tumor types

Description

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

Usage

.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

## Not run: 
plot_boxgraph_CNVratio_TCGA(c("EIF4A1", "EIF4E", "EIF4EBP1", "EIF4G1"))

## End(Not run)

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