Preprocessing, analyzing, and reporting of RNA-seq data
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Documentation for package ‘hermes’ version 1.8.0
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A C D E F G H I L M N O P Q R S T V W misc
| hermes-package | 'hermes' Package |
-- A --
| add_quality_flags | Add Quality Flags |
| all_na | Checks Whether All Missing |
| annotation | Annotation Accessor and Setter |
| annotation-method | Annotation Accessor and Setter |
| annotation<--method | Annotation Accessor and Setter |
| AnyHermesData | 'HermesData' and 'RangedHermesData' |
| AnyHermesData-class | 'HermesData' and 'RangedHermesData' |
| assertions | Additional Assertions for 'assert_that' |
| assertion_arguments | Standard Assertion Arguments |
| assert_proportion | Check for proportion |
| autoplot-method | Correlation between Sample Counts of 'AnyHermesData' |
| autoplot-method | Differential Expression Analysis |
| autoplot-method | Correlation of Principal Components with Sample Variables |
| autoplot-method | All Standard Plots in Default Setting |
| autoplot-method | Derivation of Top Genes |
-- C --
| 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 |
| colMeanZscores | Mean Z-score Gene Signature |
| colPrinComp1 | First Principal Component (PC1) Gene Signature |
| col_data_with_genes | Sample Variables with Selected Gene Information |
| ConnectionBiomart | Connection to 'BioMart' |
| ConnectionBiomart-class | Connection to 'BioMart' |
| 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 |
| correlate-method | Correlation between Sample Counts of 'AnyHermesData' |
| correlate-method | Correlation of Principal Components with Sample Variables |
| counts | Counts Accessor and Setter |
| counts-method | Counts Accessor and Setter |
| counts<--method | Counts Accessor and Setter |
| cut_quantile | Cutting a Numeric Vector into a Factor of Quantile Bins |
-- D --
| df_cols_to_factor | Conversion of Eligible Columns to Factor Variables in a 'DataFrame' |
| 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 |
-- E --
| expect_proportion | Check for proportion |
| expression_set | Example 'ExpressionSet' Data |
| extraColDataNames | Extra Variable Names Accessor Methods |
| extraColDataNames-method | Extra Variable Names Accessor Methods |
| extraRowDataNames | Extra Variable Names Accessor Methods |
| extraRowDataNames-method | Extra Variable Names Accessor Methods |
| extra_data_names | Extra Variable Names Accessor Methods |
-- F --
| filter | Filter 'AnyHermesData' on Subset Passing Default QC Flags |
| filter-method | Filter 'AnyHermesData' on Subset Passing Default QC Flags |
-- G --
| genes | Gene IDs Accessor |
| genes-method | Gene IDs Accessor |
| GeneSpec | R6 Class Representing a Gene (Signature) Specification |
| gene_spec | 'GeneSpec' Constructor |
| get_low_depth | Add Quality Flags |
| get_low_expression | Add Quality Flags |
| get_tech_failure | Add Quality Flags |
-- H --
| hermes | 'hermes' Package |
| HermesData | 'HermesData' and 'RangedHermesData' |
| HermesData-class | 'HermesData' and 'RangedHermesData' |
| HermesDataCor | Correlation between Sample Counts of 'AnyHermesData' |
| HermesDataCor-class | Correlation between Sample Counts of 'AnyHermesData' |
| HermesDataDiffExpr | Differential Expression Analysis |
| HermesDataDiffExpr-class | Differential Expression Analysis |
| HermesDataFromMatrix | 'HermesData' and 'RangedHermesData' |
| HermesDataPca | Principal Components Analysis Calculation |
| HermesDataPca-class | Principal Components Analysis Calculation |
| HermesDataPcaCor | Correlation of Principal Components with Sample Variables |
| HermesDataPcaCor-class | Correlation of Principal Components with Sample Variables |
| HermesDataSummary | Summary Method for 'AnyHermesData' Objects |
| HermesDataSummary-class | Summary Method for 'AnyHermesData' Objects |
| HermesDataTopGenes | Derivation of Top Genes |
| HermesDataTopGenes-class | Derivation of Top Genes |
| hermes_data | Example 'HermesData' Data |
| h_all_duplicated | Finding All Duplicates in Vector |
| h_cpm | Normalization of 'AnyHermesData' Objects |
| h_df_factors_with_explicit_na | Conversion to Factors with Explicit Missing Level in a 'data.frame' |
| h_diff_expr_deseq2 | 'DESeq2' Differential Expression Analysis |
| h_diff_expr_voom | 'limma'/voom Differential Expression Analysis |
| h_draw_boxplot_df | Boxplot for Gene Expression Values |
| h_ensembl_to_entrez_ids | Translation of 'Ensembl' to 'Entrez' Gene IDs |
| 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_low_depth_flag | Add Quality Flags |
| h_low_expression_flag | Add Quality Flags |
| 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 Principal Components |
| h_pca_var_rsquared | Calculation of R2 between Sample Variable and Principal Components |
| h_rlog | Normalization of 'AnyHermesData' Objects |
| h_rpkm | Normalization of 'AnyHermesData' Objects |
| h_short_list | Make a Short List of a Character Vector |
| h_strip_prefix | Stripping Prefix from Gene IDs |
| h_tech_failure_flag | Add Quality Flags |
| h_tpm | Normalization of 'AnyHermesData' Objects |
| h_unique_labels | Creation of Unique Labels |
| h_voom | Normalization of 'AnyHermesData' Objects |
| h_vst | Normalization of 'AnyHermesData' Objects |
-- I --
| inner_join_cdisc | Inner Joining a Genes with a CDISC Data Set |
| isEmpty | Checking for Empty 'SummarizedExperiment' |
| isEmpty-method | Checking for Empty 'SummarizedExperiment' |
| is_class | Additional Assertions for 'assert_that' |
| is_constant | Additional Assertions for 'assert_that' |
| is_counts_vector | Additional Assertions for 'assert_that' |
| is_hermes_data | Additional Assertions for 'assert_that' |
| is_list_with | Additional Assertions for 'assert_that' |
-- L --
| lapply | 'lapply' method for 'MultiAssayExperiment' |
| lapply-method | 'lapply' method for 'MultiAssayExperiment' |
-- M --
| metadata | Metadata Accessor and Setter |
| multi_assay_experiment | Example 'MultiAssayExperiment' Data |
-- N --
| normalize | Normalization of 'AnyHermesData' Objects |
| normalize-method | Normalization of 'AnyHermesData' Objects |
-- O --
| one_provided | Additional Assertions for 'assert_that' |
-- P --
| pca_cor_samplevar | Correlation of Principal Components with Sample Variables |
| plot_all | All Standard Plots in Default Setting |
| prefix | Prefix Accessor |
-- Q --
| query | Query Gene Annotations from a Connection |
| query-method | Query Gene Annotations from a Connection |
-- R --
| RangedHermesData | 'HermesData' and 'RangedHermesData' |
| RangedHermesData-class | 'HermesData' and 'RangedHermesData' |
| rbind | Row Binding of 'AnyHermesData' Objects |
| rename | Renaming Contents of 'SummarizedExperiment' Objects |
| rename-method | Renaming Contents of 'SummarizedExperiment' Objects |
-- S --
| samples | Sample IDs Accessor |
| samples-method | Sample IDs Accessor |
| set_tech_failure | Set Technical Failure Flags |
| show | Show Method for 'AnyHermesData' Objects |
| show-method | Show Method for 'AnyHermesData' Objects |
| show-method | Summary Method for 'AnyHermesData' Objects |
| subset | Subsetting 'AnyHermesData' Objects |
| summarized_experiment | Example 'SummarizedExperiment' Data |
| summary | Summary Method for 'AnyHermesData' Objects |
| summary-method | Summary Method for 'AnyHermesData' Objects |
-- T --
| test_proportion | Check for proportion |
| top_genes | Derivation of Top Genes |
-- V --
| validate | Internal Helper Functions for Validation of 'AnyHermesData' Objects |
| validate_cols | Internal Helper Functions for Validation of 'AnyHermesData' Objects |
| validate_col_data | Internal Helper Functions for Validation of 'AnyHermesData' Objects |
| validate_counts | Internal Helper Functions for Validation of 'AnyHermesData' Objects |
| validate_names | Internal Helper Functions for Validation of 'AnyHermesData' Objects |
| validate_prefix | Internal Helper Functions for Validation of 'AnyHermesData' Objects |
| validate_row_data | Internal Helper Functions for Validation of 'AnyHermesData' Objects |
-- W --
| wrap_in_mae | Wrap in MAE |
-- misc --
| .ConnectionBiomart | Connection to 'BioMart' |
| .HermesData | 'HermesData' and 'RangedHermesData' |
| .HermesDataCor | Correlation between Sample Counts of 'AnyHermesData' |
| .HermesDataDiffExpr | Differential Expression Analysis |
| .HermesDataPca | Principal Components Analysis Calculation |
| .HermesDataPcaCor | Correlation of Principal Components with Sample Variables |
| .HermesDataSummary | Summary Method for 'AnyHermesData' Objects |
| .HermesDataTopGenes | Derivation of Top Genes |
| .RangedHermesData | 'HermesData' and 'RangedHermesData' |
| .row_data_annotation_cols | Annotation Accessor and Setter |