Man pages for nicohuttmann/pOmics
Framework for proteomics data analysis
| add_background_variable | Add variable names in as background objects |
| add_combined_dataset | Combines variables in one dataset |
| add_data | Adds new data |
| add_database | Adds new database to .databases |
| add_dataset | Adds new datasets to list |
| add_group_columns | Helper function for df2groupedList to add column/s to the... |
| add_import | Saves imported files to .imports list |
| add_info_from_csv | Adds all info from imported csv file to observations data |
| add_observations_data | Adds data to observations data frame |
| add_observations_set | Adds a new set of observations |
| add_raw_dataset | Saves raw data frames to .info list |
| add_segment_pvalue | Adds p-values to geom_segment dataframe fo rdendrogram plot |
| add_variables_data | Add data to variables |
| adjacency | Calculates adjacency matrix from similarity matrix |
| annotation_data2list | Transforms data frame to annotation list |
| annot_layer_discrete_x | Creates discrete annotation layer |
| ask_name | Asks user for name if no name given |
| assemble_heatmap_rowwise | Combines subplots to form a heatmap |
| available_data_frames | Shows available raw data frames and returns them or prints a... |
| available_variables_data | Shows available raw variables data and returns them or prints... |
| axis_limit_breaks | Helps make nice axis limit breaks |
| bhc | Performs Benjamini-Hochberg-Correction of set of p-values |
| browse_msigdbr | Opens MSigDB entries |
| browse_proteins | Opens UniProt page of given protein |
| build_cor_list | Builds cor_list object with default parameters |
| button_begin | Creates button to hide plots and tables |
| button_end | Ends section hidden by button |
| cat_function | Prints function snippet to console and clipboard |
| cat_vector_string | Prints vectors to console in code-form |
| change_variables_manually | Allows to manually change the variables data |
| check_buttons | Sets up buttons for HTML document |
| check_database | Checks if database is available |
| choose_taxId | Helps to find taxonomy Id |
| choose_terms | Interface for user to define a list of GO terms |
| cleanup | Removes all objects except specified analysis objects |
| cluster_inner_borders | Returns borders between clusters |
| colnames_class | Returns column names from data frame of specific column class |
| colnames_typeof | Returns column names from data frame of specific column type |
| common_prefix | Finds common substring; returns "" if no characters are in... |
| compare_enrichment_data | Compares enrichment data and returns list of common and... |
| connectivity | Variable-wise connectivity |
| copy2global | Assigns all arguments with names to Global Environment |
| copy_template | Downloads template scripts and copies to clipboard |
| correct_log2fc_anova | Calculates correct log2 fold-changes to replace anova diff... |
| count_variables_per_observation | Performs analysis |
| cutree_ | Like cutree() but returns character vector |
| cv | Calculates coefficient of variation |
| cv_m | Calculates coefficient of variation |
| data2list | Pull names vector from |
| data2tibble | Transforms any data type to a tibble |
| data.frame2tibble | Transforms data frames to tibble and adds column for row... |
| data_input | Handles list input for functions |
| dendrogram | Computes a dendrogram from adjacency matrix in cor_object |
| dendrogram2table | Adds table representation of dendrogram |
| distribute_quantiles | Returns named vector and substitutes numeric values by... |
| distribute_quantiles_inner_limits | Returns named vector and substitutes numeric values by... |
| do_2w_anova_i | Performs a two-way ANOVA with an interaction term between... |
| do_abundance_summary | Template for functions that accept either a data frame or a... |
| do_annotation_composition | Calculates composition of given annotations |
| do_anova | Performs one-way ANOVA |
| do_column_summary | Collapses rows of data frame by specified function and adds... |
| do_cormat | Do a correlation matrix analysis as described by Horvath et... |
| do_count_id_quant | Combines information of identified and quantified proteins |
| do_expr | Evaluates data cell-wise |
| do_fun | Template for functions that accept either a data frame or a... |
| do_fun_enrich_dend | Template for functions that accept either a data frame or a... |
| do_GSEA | Performs gene set enrichment on numeric protein vector with... |
| do_GSEA_KEGG | Performs gene set enrichment analysis using KEGG terms |
| do_GSEA_MSigDB | Performs gene set enrichment analysis using MSigDB... |
| do_GSEA_Reactome | Performs gene set enrichment analysis using Reactome... |
| do_GSEA_topGO | Performs gene set enrichment on numeric protein vector with... |
| do_hclust | Performs hierarchical clustering on data frame |
| do_hclust_enrich_T2G | Template for functions that accept either a data frame or a... |
| do_hclust_transpose | Changes x and y dendrograms and transposes hclust data |
| do_normalize | Template for functions that accept either a data frame or a... |
| do_nothing | Template for functions that accept either a data frame or a... |
| do_ORA | Performs overexpression enrichment on logical protein vector... |
| do_ORA_GO | Performs over-representation analysis using Gene Ontology... |
| do_ORA_groups | Performs overexpression enrichment on protein group vectors |
| do_ORA_KEGG | Performs over-representation analysis using KEGG annotations |
| do_ORA_MSigDB | Performs over-representation analysis using MSigDB... |
| do_ORA_Reactome | Performs over-representation analysis using Reactome... |
| do_ORA_TERM2GENE | Performs over-representation analysis using Gene Ontology... |
| do_ORA_topGO | Performs overexpression enrichment on logical protein vector... |
| do_pca | Template for functions that accept either a data frame or a... |
| do_reverse_dend | Template for functions that accept either a data frame or a... |
| do_row_summary | Collapses rows of data frame by specified function and adds... |
| do_scale | Scales data (Z-scores) from tibbles or analysis_list... |
| dot-add_data_attributes | Adds entries to data_attributes |
| dot-data_columns | Get column names containing data independently if variables... |
| dot-get_data_attributes | Saves relevant data attributes in list |
| do_transpose | Transposes tibble and uses first column as column names |
| dot-set_data_attributes | Sets relevant data attributes from list |
| dot-template_names | Lists available template names from pOmics-templates... |
| do_t.test | Template for functions that accept either a data frame or a... |
| dot-transpose_data_attributes | Get column names containing data independently if variables... |
| dot-update_data_attributes | Compares data attributes with data and removes non-existing... |
| do_venn | Template for functions that accept either a data frame or a... |
| download_template | Downloads template scripts and writes to new file |
| enrich_dend_ | Calculates enrichment for each cluster level |
| enrich_dend_fisher | Performs Fisher's exact test on all cluster levels of given... |
| enrich_dend_ks | Performs KS test on all cluster levels of given dendrogram |
| enrichResult2data.frame | Extracts result data frame Cluster enrichResult object or... |
| eval_2w_anova_i | Classifies protein changes from two-way ANOVA with... |
| eval_anova | Evaluates data from ANOVA do_anova() for significant proteins |
| eval_dend_enrich | Evalueates dendrogram enrichment |
| export_DT_fun_enrich | Formats table for nice output (R Markdown) |
| export_DT_t.test | Formats table for nice output (R Markdown) |
| export_GO_table | Prepares GO table for output in HTML file |
| export_info_template | Exports observations names to csv info template file |
| export_pdf | Exports plot to pdf |
| export_RMD_fun_enrich | Template for functions that accept either a data frame or a... |
| export_RMD_t.test | Template for functions that accept either a data frame or a... |
| export_svg | Exports plot to svg |
| export_tiff | Exports plot to tiff |
| extract_mqpar_info | Extracts information from mqpar.xml file |
| factorize_matrix | Divides each row of a matrix by the elements of the specified... |
| find_data_entry | Identifies data entrys by column names |
| findORchoose | Finds vector entry based on given patterns and lets User... |
| first_element | Returns first element of vector |
| fisher_test | Calculates p-value from Fisher's exact test |
| fun_enrich | Performs appropriate enrichment on given sets of proteins or... |
| fun_enrich_t.test | Functional enrichment of t.test results |
| g2p | Translates gene symbols into protein accession IDs |
| geomean | Computes the geometric mean |
| get_all_attr | Prints default dataset attributes |
| get_all_variables | Returns collective variables from all datasets |
| get_child_terms | Returns all offspring terms of given GO terms |
| get_cluster_cut | Returns group information of specified number of cluster |
| get_cluster_proteins | Returns vector of proteins |
| get_cor_data | Returns data from cor_list object |
| get_data | Assemble data from dataset and return in list |
| get_database | Returns database |
| get_data_name | Check data type and return data.name |
| get_data_names | Prints or returns data names |
| get_dataset | Checks and returns correct dataset identifier |
| get_dataset_attr | Returns dataset attribute; does not check if exists |
| get_datasets | Prints or returns datasets |
| get_data_template_names | Returns existing templates for raw data |
| get_default_data_name | Return default data name |
| get_default_dataset | Get default dataset |
| get_defaults | Returns default data |
| get_GOdata | Searches for GOdata or makes new |
| get_GO_proteins | Returns GO terms from given terms |
| get_info_data | Returns .info data |
| get_input | Returns possible input names |
| get_labels_column | Checks default observations labels of no column given |
| get_MaxQuant_defaults | Returns default list for identifier and data types to import |
| get_obs | Return observations |
| get_obs_data | Return observations data |
| get_observations | Return observations |
| get_observations_data | Return observations data |
| get_observations_data_names | Returns observations data names |
| get_observations_set | Checks and returns correct observations set identifier |
| get_observations_sets | Returns observations sets |
| get_observations_template | Creates template for new variables data |
| get_OrgDb | Checks organism database name from Bioconductor and if... |
| get_protein | NOT DONE |
| get_protein_list | Returns lists of proteins |
| get_proteins_TERM2GENE | Retrieves proteins from annotation terms |
| get_proteome | Returns all proteome accession numbers of given sepcies |
| get_raw_dataset | Returns raw datasets from .info list |
| get_taxId | Identifies taxonomy Id if possible, ask otherwise |
| get_var | Return variables |
| get_variables | Return variables |
| get_variables_data | Return variables data |
| get_variables_data_names | Returns variables data names |
| get_variables_template | Creates template for new variables data |
| gg_extract_legend | Extract legend from ggplot object |
| gg_legend.position | Removes or repositions legend of ggplot |
| gg_size | Corrects size to points in ggplots |
| identify_data_origin | Identifies MS spectra analysis software |
| identify_observations | Guesses observations names from raw_dataset |
| identify_separator | Identifies most common character from dataset and tests for... |
| identify_taxId | Checks protein Ids for their species |
| identify_variables | Finds feasible identifier columns |
| import2grouped_data | Stores data frame in a list and groups adjacent columns |
| import2raw_dataset | Extracts variables and grouped data from imported data frame |
| import_fasta | Imports fasta file and saves proteome |
| import_files | Imports any file type using the file extension and returns... |
| import_Top100_EV | Downloads Top100 protein list and converts to protein... |
| impute_missForest | Imputes missing values based on a Random Forest algorithm |
| impute_norm | Imputes values based on normal distribution |
| in_ | Intersects x and y, but keeps names from x |
| include_groups | Adds group vector to data frame |
| include_observations_data | Adds group vector to data frame |
| include_variables_data | Adds group vector to data frame |
| initialize_data_structure | Creates basic data structure |
| intersect_m | Intersect multiple vectors |
| is_data_name | Check if data name exists |
| is_data_origin | Checks if given data.origin is among the defaults |
| is_dataset | Check if dataset exists |
| is_info_data | Checks if .info data exists |
| is_observations_data | Checks if observations data exists |
| is_observations_set | Checks if observations set exists |
| is_raw_dataset | Check if raw_dataset exists |
| is_variables_data | Checks if variables data name exist |
| ks_test | Calculates p-value from Fisher's exact test |
| last_ | Returns first element of vector |
| latex_abbr_table | Prints latex table code to console (made for abbreviations... |
| list2group_vector | Transforms list to group vector for functional enrichment |
| list2tibble | Transforms a list to tibble logical indication for variables |
| list_entries2vector | Transforms list entries to vector of one element each;... |
| list_files | Returns all files in the Data folder excluding RData |
| load_msigdb_data | Extracts category specific TERM2GENE data frames from local... |
| map_variables | Return variables by matching variables.data |
| map_variables_data | Return variables by matching variables.data |
| match_v2l | Matches vector entries to list (stackoverflow question... |
| matrix2tibble | Transforms matrix to tibble and adds column for row names |
| matrix_rows | Subsets matrix by rownames and checks for transformations... |
| mean_or_0 | Helper function to combine technical replicates (only returns... |
| merge_enrichResults | Merges a (nested) list of enrichResult objects |
| merge_TERM2GENE | Combines TERM2GENE dataframes |
| most_common_character | Finds and returns most common character in a data |
| new_analysis_list | Add or replace analysis list |
| new_cache | Creates new cache list |
| new_databases_list | Creates databases list |
| new_dataset | Sorts raw data into data list with attributes |
| new_datasets_list | Creates datasets list |
| new_default_data | Add default dataframe if it does not exist |
| new_imports_list | Creates imports list |
| new_info_list | Creates new info list |
| next_button | Increases button count |
| nice_number | Help make nice number in R Markdown |
| normalize | Normalizes and returns data |
| nulllist | Returns list filled with NULL of n length |
| p2g | Returns gene symbol from known proteins in dataset |
| p2n | Returns names from known proteins |
| paste_terms_overlap_heatmap | Combines names and count of annotation terms |
| plot_bar_composition | Plots data as bar plot with ggplot2 |
| plot_ComplexHeatmap | Template for functions that accept either a data frame or a... |
| plot_cormat | Plots correlation matrix with dendrograms |
| plot_count_id_quant | Barplot of identified/quantified proteins per sample |
| plot_dend_enrich_lines | Plots -log10 p-value profile of dendrogram enrichment |
| plot_enrich | TPlots lines and cormat enrichment |
| plot_enrichment_barplot | Plots barplot as used by clusterProfiler |
| plot_euler | Plots Euler diagram from dataframe |
| plot_gg_bar | Plots data as bar plot with ggplot2 |
| plot_gg_bar_anova_eval | Plots stacked bar plot to indicate significantly changed... |
| plot_gg_count_id_quant | Barplot of identified/quantified proteins per sample |
| plot_gg_heatmap_protein_overlap | Compares log2 fold-changes between two comparisons from an... |
| plot_gg_heatmap_terms | Plots heatmap with dendrograms |
| plot_gg_xy_fc | Compares log2 fold-changes between two comparisons from an... |
| plot_heatmap | Plots heatmap with dendrograms |
| plot_heatmap_discrete | Plots heatmap with dendrograms |
| plot_lines | Lines plot fo rpublication in ggplot2 |
| plot_nothing | Template for functions that accept either a data frame or a... |
| plot_pca | Plots PCA with ggplot2 |
| plot_upset | Visualizes identification data as UpSet plot |
| plot_venn | Plots a venn diagram form given data |
| plot_volcano | Plots a volcano plot with ggplot2 |
| plot_xy | Matches names and plots scatter plot of two variables |
| pqn | Probabilistic quotient normalization |
| prep_data | Prepares data for analysis |
| print_options | Prints options similar to menu() function |
| protein2function | Returns list vector of protein functions from UniProt |
| protein2gene | Translates protein accession Ids to gene names |
| pull_data | Pull names vector from |
| put_data | Assemble data from dataset and return in list |
| quick_protein_count | Wrapper around do_count_id_quant |
| remove_dataset | Removes dataset |
| remove_observations_data | Removes observations data |
| remove_variables | Removes columns from data frame based on minimum values above... |
| remove_variables_data | Removes variables data |
| reorder_data | Reorders dataframe rows according to observations data order |
| rm_functions | Removes functions from global environment |
| same_prefix | Test vector of strings for a common prefix of minimal given... |
| save2cache | Saves data in cache |
| save_results | Store analysis object in Analysis list |
| save_wd | Saves given or current working directory |
| select2output | Formats mapping from select methods |
| select_DisGeNet | Improved select function for DisGeNet databases |
| select_fasta | Retrieve annotation data from imported fasta files |
| select_org | Queries data from Annotation packages |
| select_org_2_TERM2GENE | Exports TERM2GENE dataframe from select_org |
| select_UniProt | Improved select function for UniProt databases |
| select_UniProt_2_TERM2GENE | Exports TERM2GENE dataframe from select_org |
| sep_vector2list | # Generates a list from separated vector |
| set_continuous_axes | Defines ggplot panel by ratio, size, unit size, center, and... |
| set_dataset_attr | Sets dataset attribute; does not check if exists |
| set_default_data_name | Set default data name |
| set_default_dataset | Updates default dataset |
| set_default_observations_set | Set default data set |
| set_diagonal | Sets diagonal values of symmetric matrix |
| setup_CORUM_annotations | Downloads CORUM database for functional enrichment |
| setup_DisGeNET | Registers API key to use disgenet2r... |
| setup_EV_TOP_100 | Downloads Top 100 EV protein markers from Vesiclepedia |
| setup_folders | Creates folder structure for analysis project |
| setup_fun_enrich | Initiates databases for functional enrichment |
| setup_msigdb | Downloads and prepares MSigDB annotations |
| setup_org_database | Sets up annotaion database for biological Id translation and... |
| setup_STRINGdb | Sets up the STRING database |
| setup_taxonomy_information | Sets up annotaion database for biological Id translation and... |
| setup_UniProt | Loads the species specific UniProt.ws to the .GlobalEnv |
| set_wd | Changes working directory |
| significant | Returns logical vector indication significant p-values |
| similarity | Calculates similarity from correlation |
| simplify_enrichment_results | Simplifies enrichment data frame by overlap between... |
| simplify_GO_terms_semantic | Removes similar GO terms and keeps terms in order (assumes... |
| simplify_set_overlap | Removes similar protein sets based on minimum overlap |
| str_locate_last | Locates last position of pattern in given string |
| str_rev | Returns given strings in reverse order |
| strsplit_ | Same as strsplit but option to return as vector and to... |
| strsplit_keep | Performs strsplit and keeps elements specified by vector |
| strsplit_keep_first | Performs strsplit and keeps first element of each string |
| strsplit_keep_firstn | Performs strsplit and keeps first n elements of each string |
| subset_observations | Removes columns from data frame based on minimum values above... |
| subset_variables | Removes columns from data frame based on minimum values above... |
| summary_proteins | Views a list of proteins |
| summary_proteins_2 | Views a list of proteins with links to UniProt |
| t2g_get_genes | Get vector or list of genes mapped to given term/s |
| t2g_get_matrix | Get tibble of terms mapped to genes |
| t2g_get_terms | Get vector or list of terms mapped to given gene/s |
| t2g_subset_genes | Subset term-to-gene data frame by given genes |
| t2g_subset_terms | Subset term-to-gene data frame by given terms |
| TERM2GENE_2_list | Splits TERM2GENE dataframe to list |
| TERMS_in_proteins | Returns logical dataframe which proteins is annotated by... |
| theme_epitope_peptides_plot | Create a theme for half open plots for Hjv project |
| theme_hjv_framed | Create a theme for half open plots for Hjv project |
| theme_hjv_framed_no_axes | Create a theme for half open plots for Hjv project |
| theme_hjv_half_open | Create a theme for half open plots for Hjv project |
| theme_hjv_heatmap | Create a theme for heatmaps for Hjv project |
| theme_hjv_heatmap_only | Create a theme for half open plots for Hjv project |
| theme_hjv_heatmap_only_noframe | Create a theme for half open plots for Hjv project |
| theme_hjv_overlap_heatmap | Create a theme for half open plots for Hjv project |
| theme_iDC_annot_layer | Create a theme for half open plots for Hjv project |
| theme_iDC_dendrogram | Create a theme for half open plots for Hjv project |
| theme_iDC_heatmap_labels_x | Create a theme for half open plots for Hjv project |
| theme_iDC_heatmap_labels_y | Create a theme for half open plots for Hjv project |
| theme_iDC_heatmap_w_legend | Create a theme for half open plots for Hjv project |
| theme_phosprot_half_open | Create a theme for half open plots for Hjv project |
| theme_thesis_cor_matrix | Create a theme for half open plots for Hjv project |
| theme_thesis_framed_no_axis | Create a theme for half open plots for Hjv project |
| threshold | Returns logical vector indicating values above or below given... |
| tibble2data.frame | Transforms tibble to data frame |
| tibble2matrix | Transforms tibble to matrix |
| to_data_ | Adds data to data_ list |
| total_proteins_summary | INCOMOPLETE FUNCTION: Combines data frames with variables... |
| transfer_data_frames | Transfers data from raw_dataset to .datasets |
| transfer_observations | Transfers observations from raw_dataset to .datasets |
| transfer_variables_data | Transfers variables data from raw_dataset to .datasets |
| translate_Ids | Translates biological IDs using annotations packages |
| transpose_tibble | Transposes tibble and uses first column as column names |
| useful_UniProt_entries | Prints useful/working UniProt entries |
| variables2labels | Wrapper around get_variables_data to replace variables with... |
| v_db | Shows databases list |
| v_ds | Shows datasets list |
| view_data | Shows all data lists |
| view_default_attr | Prints default dataset attributes |
| view_observations | Prints observations data frame |
| view_variables | Prints variables data frame |
| v_imp | Shows imports list |
| v_info | Shows info list |
| which_names | Returns names of TRUE vector elements |
