dot-plot_bargraph_CNV_TCGA: Summary of CNV statuses in bar plots

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

Summary of CNV statuses in bar plots

Description

Provides the summary of CNV statuses of EIF4F genes in tumors from all TCGA cancer types combined and in tumors from individual TCGA cancer types

Usage

.plot_bargraph_CNV_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_CNV_sampletype - a global variable generated from initialize_cnv_data().

• uses the subset data .TCGA_CNV_sampletype_subset to perform the CNV status analysis of all inquired genes with the internal functions .CNV_all_cancer() and plot the results as a bar plot with the internal function .CNV_sum_barplot().

• uses the same subset data .TCGA_CNV_sampletype_subset to perform CNV status analysis for each gene across all tumors types by the internal function .CNV_ind_cancer() and plots the CNV results by the internal function .CNV_barplot().

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 stacked bar plots on screen and as pdf files to show the summary table of the CNV statuses of all gene_list in TCGA tumors

(2) stacked bar plots on screen and as saved pdf files to show CNV status of each gene in gene_list from an individual cancer type

See Also

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

Examples

## Not run: 
plot_bargraph_CNV_TCGA(c(
  "TP53", "EIF4A1", "EIF4A2", "EIF4E",
  "EIF4E2", "EIF4E3", "MYC", "EIF3D", "EIF4EBP1", "EIF4G1", "EIF4G2",
  "EIF4G3", "PABPC1", "MKNK1", "MKNK2"
))

## End(Not run)

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