Man pages for insightsengineering/hermes
Preprocessing, analyzing, and reporting of RNA-seq data
| all_na | Checks Whether All Missing |
| annotation | Annotation Accessor and Setter |
| assertion_arguments | Standard Assertion Arguments |
| assertions | Additional Assertions for 'assert_that' |
| calc_cor | Correlation between Sample Counts of 'AnyHermesData' |
| calc_pca | Principal Components Analysis Calculation |
| cat_with_newline | Concatenate and Print with Newline |
| cbind | Column Binding of 'AnyHermesData' Objects |
| check_proportion | Check for proportion |
| col_data_with_genes | Sample Variables with Selected Gene Information |
| colMeanZscores | Mean Z-score Gene Signature |
| colPrinComp1 | First Principal Component (PC1) Gene Signature |
| connect_biomart | Connection to 'BioMart' |
| control_normalize | Control Settings for Counts Normalization |
| control_quality | Control for Specified Quality Flags |
| correlate | Generic Function for Correlation Calculations |
| counts | Counts Accessor and Setter |
| cut_quantile | Cutting a Numeric Vector into a Factor of Quantile Bins |
| df_cols_to_factor | Conversion of Eligible Columns to Factor Variables in a... |
| diff_expression | Differential Expression Analysis |
| draw_barplot | Barplot for Gene Expression Percentiles |
| draw_boxplot | Boxplot for Gene Expression Values |
| draw_genes_barplot | Stacked Barplot of Low Expression Genes by Chromosome |
| draw_heatmap | Heatmap for Gene Expression Counts |
| draw_libsize_densities | Density Plot of (Log) Counts Distributions |
| draw_libsize_hist | Histogram of Library Sizes |
| draw_libsize_qq | Q-Q Plot of Library Sizes |
| draw_nonzero_boxplot | Boxplot of Non-Zero Genes |
| draw_scatterplot | Scatterplot for Gene Expression Values |
| expression_set | Example 'ExpressionSet' Data |
| extra_data_names | Extra Variable Names Accessor Methods |
| filter | Filter 'AnyHermesData' on Subset Passing Default QC Flags |
| genes | Gene IDs Accessor |
| gene_spec | 'GeneSpec' Constructor |
| GeneSpec | R6 Class Representing a Gene (Signature) Specification |
| h_all_duplicated | Finding All Duplicates in Vector |
| h_df_factors_with_explicit_na | Conversion to Factors with Explicit Missing Level in a... |
| h_diff_expr_deseq2 | 'DESeq2' Differential Expression Analysis |
| h_diff_expr_voom | 'limma'/voom Differential Expression Analysis |
| h_ensembl_to_entrez_ids | Translation of 'Ensembl' to 'Entrez' Gene IDs |
| hermes_data | Example 'HermesData' Data |
| HermesData-class | 'HermesData' and 'RangedHermesData' |
| hermes-package | 'hermes' Package |
| h_get_annotation_biomart | Get Annotations from 'BioMart' |
| h_get_granges_by_id | Conversion of 'BioMart' Coordinates into 'GRanges' |
| h_get_size_biomart | Total Length of All Exons for Genes |
| h_has_req_annotations | Predicate for Required Annotations |
| h_map_pos | Helper Function For Matching Map Values to Names |
| h_parens | Parenthesize a Character Vector |
| h_pca_df_r2_matrix | Calculation of R2 Matrix between Sample Variables and... |
| h_pca_var_rsquared | Calculation of R2 between Sample Variable and Principal... |
| h_short_list | Make a Short List of a Character Vector |
| h_strip_prefix | Stripping Prefix from Gene IDs |
| h_unique_labels | Creation of Unique Labels |
| inner_join_cdisc | Inner Joining a Genes with a CDISC Data Set |
| isEmpty | Checking for Empty 'SummarizedExperiment' |
| lapply | 'lapply' method for 'MultiAssayExperiment' |
| metadata | Metadata Accessor and Setter |
| multi_assay_experiment | Example 'MultiAssayExperiment' Data |
| normalize | Normalization of 'AnyHermesData' Objects |
| pca_cor_samplevar | Correlation of Principal Components with Sample Variables |
| pipe | Pipe operator |
| plot_all | All Standard Plots in Default Setting |
| prefix | Prefix Accessor |
| quality_flags | Add Quality Flags |
| query | Query Gene Annotations from a Connection |
| rbind | Row Binding of 'AnyHermesData' Objects |
| rename | Renaming Contents of 'SummarizedExperiment' Objects |
| samples | Sample IDs Accessor |
| set_tech_failure | Set Technical Failure Flags |
| show | Show Method for 'AnyHermesData' Objects |
| subset | Subsetting 'AnyHermesData' Objects |
| summarized_experiment | Example 'SummarizedExperiment' Data |
| summary | Summary Method for 'AnyHermesData' Objects |
| top_genes | Derivation of Top Genes |
| validate | Internal Helper Functions for Validation of 'AnyHermesData'... |
| wrap_in_mae | Wrap in MAE |
