Man pages for HCGB-IGTP/HCGB.IGTP.DAnalysis
Useful in-house functions for multiple analysis
| adjust_samples | Adjust sample names |
| analysis_DESeq | DESEQ2 analysis pipeline |
| beta_values_plots | BetaDistribution plots |
| check_covariates | Check for covariates using RnBead object |
| check_rank_design | Check the rank of a design matrix |
| check_reduced_LRT | Check the effect of reducing one term from a DESEQ2 design |
| check_terms_matrix | Check the effect of variables in matrix design |
| colnames_GRanges | Get column names for a GRanges object |
| convertDate | Convert Spanish date: 14/5/2022 into English american format:... |
| create_col_palette | Assigns color codes for samples |
| create_matrix_overlaps | Create matrix of region overlaps |
| create_matrix_overlaps_by_seqnames | Create matrix of region overlaps (by sequence) |
| create_overlaps | Create overlaps for a GR vs. list of GRs |
| create_report | Annotates GR Report for each region of bumps provided |
| create_upset | Creates UpSetR plot |
| create_upset_data | Create UpSetR plot dataframe |
| create_upset_plot | Plots UpSetR |
| custom_annotation | Loads custom annotation |
| delete_na | Remove NAs in dataframe |
| DESeq2_HCGB_function | DESEq2 main function |
| df.factorizer | Converts columns in factors |
| dim_GRanges | Get dimensions for a GRanges object |
| discard_0_counts | Discard empty counts |
| discard_lowCounts | This functions discard low counts in a DESeq object. Uses 10... |
| discard_lowCounts_df | Discard low counts in dataframe |
| dreduction_function | Creates dimension reduction plots using RnBead object |
| enricher_loop | Create gene ontology enrichment for a given dataset |
| exploratory_plots | Exploratory plots for DESEQ2 analysis |
| FGSEA_GSEA | FGSEA enrichment analysis |
| FGSEA_GSEA_loop | Create GSEA loop |
| filter_bump_table | Filter bumps and retain more significant |
| filter_dmpFinder_table | Filter dmpFinder methylation stats |
| filter_signficant_DESEQ | Filter significant hits from DESEQ2 analysis |
| filter_signficant_limma | Filter limma DE analysis |
| get_all_data_DESeq2 | Get results from DESeq2 and normalized data |
| get_beta_mean_vals | Get mean beta values for two list of samples |
| get_chr_len | Return dataframe with chromosome length for hg19 genome |
| get_cols | Get cols of dataframe |
| get_comparison_resultsNames | Get names provided in comparison |
| get_data_upset | Get files for UpSetR plot Get information of interest to... |
| get_dim.filt | Title |
| get_freq | Get the frequency of elements in a vector |
| get_gene_annotation | Get gene annotation from BioMart |
| get_gene_coordinates | Get gene coordinates from BioMart |
| get_GSEA_datasets | Get GSEA Datasets |
| get_length_vect | Get the length of unique elements in a vector |
| get_limma_results | Create limma DE analysis for all coefficients |
| get_pfb | Get PFB information |
| get_probes_limma | Create limma analysis for each probe |
| get_Results_DDS | Generate results given a DDS object |
| get_rows | Get rows of dataframe |
| get_single_UpSet_plot | Get UpSetR unique intersect |
| get_topGO_data | Create topGO data and enrichment analysis |
| get_vect | Get the unique elements in a vector |
| ggboxplot_scatter | Shorcut to using ggscatterBoxplots |
| ggscatter_plotRegression | Shorcut to using ggscatter regression plots |
| gprofiler_analysis | Create gprofiler gene ontology enrichment for a given dataset |
| GRanges_subsetter | Subset lisf ot GRanges objects |
| grapes-not-in-grapes | Get the not included in |
| GR_list_samples | Create GR list subseting dataframe |
| limma_DE_function | Create limma DE analysis |
| litfover_func | Convert hg19 <-> hg38 coordinates |
| load_beta_values | Load Beta Values |
| loader | Loads R data into variable |
| load_RnBeads_object | Loads RnBead object |
| locus_plotter | RnBeads Locus plotter caller |
| maplot | Create MA plot |
| my_volcanoplot_region | VolcanoPlot region |
| my_volcanoplot_sites | VolcanoPlot site |
| pheatmap_log | Title |
| plot_batch_effect | Plot batch effect |
| plotCN.here | Extended genoCN plot for BAF and LRR |
| plotCN_zoom | Extended genoCN plot for BAF and LRR using a Zoom region |
| plot_control_means | Function to create single plots by control probe category |
| plot_DESeq2_pvalues | Plot DESeq2 p-values |
| plot_genes | RnBeads Locus plotter dataframe |
| plot_gene_values | Plot values per genes |
| plot.grid.ggscatterBoxplot | Grid plots using ggscatterBoxplots |
| plot.grid.ggscatterRegression | Grid plots using ggscatter regression |
| plot_GSEA | Plog GSEA |
| plot_representation | Create PCA/UMAP plot |
| print_plot_control_means | Create control probe plots |
| produce_norm_plots | Improve norm plots generated by meffil |
| rank_list_by | Rank table by given variable |
| read_genoCN | Read genoCN output file |
| read_pennCNV | Read pennCNV output file |
| relevel_function | Relevel and rung DESEQ2 analysis |
| save_bed_info | Save BUMP information in BED file format |
| save_jpeg | Save plots in JPEG format |
| save_norm_plots | Save and improve norm plots generated by meffil |
| save_pdf | Save plot in pdf |
| save_plots_multiformat | Save plots in multiple formats |
| save_png | Save plots in PNG format |
| save_qc_plots | Save QC summary plots as PDF |
| save_RnBeads_object | Saves RnBead object |
| sessionInfo_write | Saves R sessionInfo data into file |
| vector_splitter | Split vector into parts |
| volcanoplot | Create Volcano plot |
| write_norm_files | Save txt file for normalization objects |
| write_qc_files | Function to save txt information from meffil QC analysis |
