R/COR.R
dot-plot_Corr_RNAseq_TCGA_GTEX.RdThis function
finds correlating genes of EIF4F from the data frame TCGA_GTEX_RNAseq_sampletype
a global variable generated by initialize_RNAseq_data().
identifies positively or negatively correlating genes from tumor or
healthy samples by .EIF_correlation(),
finds the overlap of CORs for EIF4F subunits with .CORs_vennplot(),
compares the number of CORs for EIF4F subunits with
.combine_CORs_summary() and plot the results in bargraph
with .CORs_summary_bargraph()
compares the correlation strength of CORs from healthy tissues and tumors
from merged data frame generated from .combine_CORs_list() and visualizes
clustering results in heatmap with .CORs_coeff_heatmap()
retrieve the gene names from the clusters in heatmap with
.get_cluster_genes()
performs the pathways enrichment analysis on the retrieved gene list and
plot the results with .pathway_dotplot()
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_Corrgene_analysis()
function.
Side effects:
(1) Venn diagrams on screen and as pdf file to show the overlap of
EIF correlating genes identify from RNAseq of tissue_type
(2) bar graphs on screen and as pdf file to show the numbers of
identified correlating genes for each EIF4F subunit identify from
RNAseq of tissue_type
(3) heatmap on screen and as pdf file to show correlation strength and clustering pattern of EIF4F correlating genes
(4) dotplot on screen and as pdf file to show the enriched pathways in the genes from different clusters in the heatmap
.plot_Corr_RNAseq_TCGA_GTEX(tissue_type)all tissue/tumor types or one specific type
if (FALSE) {
.plot_Corr_RNAseq_TCGA_GTEX(x = "All")
.plot_Corr_RNAseq_TCGA_GTEX(x = "Lung")
}