Man pages for a3609640/eIF4F.analysis
A R package to analyze eIF4F subunits in human cancers
| color | Generates a number of most distinctive colors. |
| dot-biplot | Plot PCA results as biplot, scree and matrix plots |
| dot-biplot_title | Generate title for PCA plots |
| dot-CNV_all_cancer | Calculates the frequency of CNV status in all TCGA cancer... |
| dot-CNV_barplot | Stacked bar plots of the CNV status |
| dot-CNV_ind_cancer | Calculates the frequency of CNV status in individual TCGA... |
| dot-CNVratio_boxplot | Box plots of the CNV ratios in tumors vs adjacent normals |
| dot-CNVratio_tumor | Calculates the frequency of CNV status in all TCGA cancer... |
| dot-CNV_sum_barplot | Stacked bar plots of the CNV status summary |
| dot-combine_CORs_list | Combine all the EIF4F correlating gene data from tumor and... |
| dot-combine_CORs_summary | Combine the summary of number of posCORs or negCORs from... |
| dot-correlation_coefficient | Calculate the correlation co-efficiency between two gene... |
| dot-CORs_coeff_heatmap | Visualize associations between different sources of... |
| dot-CORs_summary_bargraph | Plot bargraph for the numbers of correlating genes |
| dot-CORs_vennplot | Plot Venn diagrams for correlating genes |
| dot-EIF_correlation | Identify EIF4F correlating genes |
| dot-forest_graph | Forest plots of COX-PH results |
| dot-get_CCLE_Proteomics_subset | Select subset of CCLE proteomics data |
| dot-get_CCLE_RNAseq_subset | Select subset of CCLE RNAseq data |
| dot-get_cluster_genes | Retrieve the gene names from each cluster in heatmap |
| dot-get_CPTAC_LUAD_Phosproteomics_subset | Select subset of CPTAC phosproteomics data |
| dot-get_CPTAC_LUAD_Proteomics_subset | Select subset of CPTAC proteomics data |
| dot-get_df_subset | Select RNAseq data based on the sample types |
| dot-get_TCGA_CNV | Read CNV threshold dataset from TCGA |
| dot-get_TCGA_CNV_ratio | Read CNV ratio dataset from TCGA |
| dot-get_TCGA_CNV_value | Read CNV value dataset from TCGA |
| dot-get_TCGA_GTEX_RNAseq | Read recomputed RNAseq data from both TCGA and GTEx |
| dot-get_TCGA_RNAseq | Read the RNAseq data from TCGA |
| dot-is_significant_correlation | Select both positive and negative correlating genes based on... |
| dot-is_significant_negcor | Select negative correlating genes based on coefficiency and... |
| dot-is_significant_poscor | Select positive correlating genes based on coefficiency and... |
| dot-KM_curve | Kaplan Meier survival analyses of gene expression |
| dot-matrix_plot | Correlation matrix for gene pairs |
| dot-multivariable_analysis | Multivariable Cox-PH analyses of gene expression |
| dot-pathway_dotplot | Plot the enriched pathways from gene lists |
| dot-plot_bargraph_CNV_TCGA | Summary of CNV statuses in bar plots |
| dot-plot_boxgraph_CNVratio_TCGA | CNV ratios in tumors vs adjacent normal tissues across tumor... |
| dot-plot_boxgraph_protein_CPTAC | Comparison of protein and phosphorylation levels among... |
| dot-plot_boxgraph_RNAratio_TCGA | Compare the RNA ratios between EIF4F genes |
| dot-plot_boxgraph_RNAseq_TCGA | Compare the expression of EIF4F genes |
| dot-plot_Corr_RNAseq_TCGA_GTEX | Perform correlation analysis on RNAseq data from all tumors... |
| dot-plot_CoxPH_RNAseq_TCGA | Survival analyses of TCGA patients with expression in their... |
| dot-plot_KM_RNAseq_TCGA | Survival analyses of TCGA patients with expression in their... |
| dot-plot_matrix_CNVcorr_TCGA | Correlation matrix for CNV values |
| dot-plot_PCA_CPTAC_LUAD | Perform PCA on proteomics data from CPATC LUADs and matched... |
| dot-plot_PCA_TCGA_GTEX | Perform PCA on RNAseq data from all tumors and healthy... |
| dot-plot_PCA_TCGA_GTEX_tumor | Perform PCA on RNAseq data from one tumor type and its... |
| dot-plot_scatterplot_protein_CPTAC | protein-protein coexpression in CPTAC LUAD |
| dot-plot_scatter_RNApro_CCLE | Correlation between CCLE RNAseq and proteomics data |
| dot-plot_scatter_RNApro_LUAD | Correlation between LUAD RNAseq and proteomics data |
| dot-protein_boxplot | Boxplots of phosphor-proteomics data across clinic stages |
| dot-protein_imputePCA | Perform imputPCA on proteomics data |
| dot-protein_scatterplot | Scatter plots of protein coexpression |
| dot-RNApro_scatterplot | Scatter plots of correlation between RNAseq and proteomics... |
| dot-RNAratio_boxplot | Box plots of differential RNA ratios across tumors |
| dot-RNAratio_calculation | Calculate RNA ratios |
| dot-RNAratio_selection | Select RNA ratio data for plotting |
| dot-RNAratio_tumortype | Analyzes differential RNA ratios in primary, metastatic... |
| dot-RNAseq_all_gene | Compares expressions among genes in tumor samples |
| dot-RNAseq_boxplot | Box plots of differential gene expression across tumors |
| dot-RNAseq_grouped_boxplot | Grouped box plots of RNA expression across tumors |
| dot-RNAseq_ind_gene | Analyzes differential gene expression in tumors vs adjacent... |
| dot-RNAseq_PCA | Perform PCA on RNAseq data |
| dot-RNAseq_tumortype | Select gene expression data in primary, metastatic tumors vs... |
| dot-selected_biplot | Plot subgroups of PCA results as biplots |
| dot-summarize_counts | Summary of total number of CORs identified for each EIF4F... |
| dot-univariable_analysis | Univariable Cox-PH analyses of gene expression |
| dot-violinplot | Violin plots of differential gene expression/ratio in... |
| eIF4F.analysis-package | eIF4F.analysis: A R package to analyze eIF4F subunits in... |
| EIF4F_CNV_analysis | Perform all CNV related analysis and generate plots |
| EIF4F_Corrgene_analysis | Perform differential correlation analyses and generate plots |
| EIF4F_DEG_analysis | Perform differential gene expression or ratio analysis and... |
| EIF4F_PCA | Perform PCA and generate plots |
| EIF4F_Proteomics_analysis | Analyze co-expression among EIF4F subunits and differential... |
| EIF4F_RNA_pro_correlation | Perform RNA protein correlation and generate scatter plots |
| EIF4F_Survival_analysis | Perform all related survival analysis and generate plots |
| initialize_cnv_data | Read all CNV related datasets from TCGA |
| initialize_data | A wrapper function reads datasets from the download data... |
| initialize_dir | Set output directories |
| initialize_format | Set format for font and color of plots |
| initialize_phosphoproteomics_data | Read all phosphoproteomics related datasets from CPTAC LUAD |
| initialize_proteomics_data | Read all proteomics related datasets from CCLE and CPTAC LUAD |
| initialize_RNAseq_data | Read all RNA-seq related datasets from TCGA and GTEx |
| initialize_survival_data | Read RNA-seq and survival datasets from TCGA |
| pipe | Pipe operator |
