Function reference • hermes

Package
`hermes-package`	`hermes` Package
Classes
`HermesData()` `HermesDataFromMatrix()`	`HermesData` and `RangedHermesData`
`correlate(<AnyHermesData>)` `autoplot(<HermesDataCor>)`	Correlation between Sample Counts of `AnyHermesData`
`calc_pca()`	Principal Components Analysis Calculation
`top_genes()` `autoplot(<HermesDataTopGenes>)`	Derivation of Top Genes
`summary()` `show(<HermesDataSummary>)`	Summary Method for `AnyHermesData` Objects
`correlate(<HermesDataPca>)` `autoplot(<HermesDataPcaCor>)`	Correlation of Principal Components with Sample Variables
`diff_expression()` `autoplot(<HermesDataDiffExpr>)`	Differential Expression Analysis
`connect_biomart()`	Connection to BioMart
`GeneSpec`	R6 Class Representing a Gene (Signature) Specification
Constructors
`HermesData()` `HermesDataFromMatrix()`	`HermesData` and `RangedHermesData`
`gene_spec()`	`GeneSpec` Constructor
Internal Helper Functions
`all_na()`	Checks Whether All Missing
`cat_with_newline()`	Concatenate and Print with Newline
`validate_counts()` `validate_cols()` `validate_row_data()` `validate_col_data()` `validate_names()` `validate_prefix()`	Internal Helper Functions for Validation of `AnyHermesData` Objects
`h_map_pos()`	Helper Function For Matching Map Values to Names
`normalize(<AnyHermesData>)` `h_cpm()` `h_rpkm()` `h_tpm()` `h_voom()` `h_vst()` `h_rlog()`	Normalization of `AnyHermesData` Objects
`add_quality_flags()` `h_low_expression_flag()` `h_low_depth_flag()` `h_tech_failure_flag()` `get_tech_failure()` `get_low_depth()` `get_low_expression()`	Add Quality Flags
`h_diff_expr_voom()`	`limma`/`voom` Differential Expression Analysis
`h_diff_expr_deseq2()`	DESeq2 Differential Expression Analysis
`h_pca_var_rsquared()`	Calculation of R2 between Sample Variable and Principal Components
`h_pca_df_r2_matrix()`	Calculation of R2 Matrix between Sample Variables and Principal Components
`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_ensembl_to_entrez_ids()`	Translation of Ensembl to Entrez Gene IDs
`h_strip_prefix()`	Stripping Prefix from Gene IDs
`h_has_req_annotations()`	Predicate for Required Annotations
`h_short_list()`	Make a Short List of a Character Vector
`h_parens()`	Parenthesize a Character Vector
`h_all_duplicated()`	Finding All Duplicates in Vector
`h_unique_labels()`	Creation of Unique Labels
`h_df_factors_with_explicit_na()`	Conversion to Factors with Explicit Missing Level in a `data.frame`
`draw_boxplot()` `h_draw_boxplot_df()`	Boxplot for Gene Expression Values
Example Data
`expression_set`	Example `ExpressionSet` Data
`hermes_data`	Example `HermesData` Data
`summarized_experiment`	Example `SummarizedExperiment` Data
`multi_assay_experiment`	Example `MultiAssayExperiment` Data
Methods
`annotation(<AnyHermesData>)` `.row_data_annotation_cols` `annotation<-`(<AnyHermesData>,<DataFrame>)	Annotation Accessor and Setter
`cbind`	Column Binding of `AnyHermesData` Objects
`correlate()`	Generic Function for Correlation Calculations
`counts(<AnyHermesData>)` `counts<-`(<AnyHermesData>,<matrix>)	Counts Accessor and Setter
`extraColDataNames()` `extraRowDataNames()`	Extra Variable Names Accessor Methods
`filter()`	Filter `AnyHermesData` on Subset Passing Default QC Flags
`genes()`	Gene IDs Accessor
`isEmpty(<SummarizedExperiment>)`	Checking for Empty `SummarizedExperiment`
`lapply(<MultiAssayExperiment>)`	`lapply` method for `MultiAssayExperiment`
`metadata`	Metadata Accessor and Setter
`normalize(<AnyHermesData>)` `h_cpm()` `h_rpkm()` `h_tpm()` `h_voom()` `h_vst()` `h_rlog()`	Normalization of `AnyHermesData` Objects
`prefix()`	Prefix Accessor
`query()`	Query Gene Annotations from a Connection
`rbind`	Row Binding of `AnyHermesData` Objects
`rename(<SummarizedExperiment>)` `rename(<data.frame>)`	Renaming Contents of `SummarizedExperiment` Objects
`samples(<AnyHermesData>)`	Sample IDs Accessor
`show(<HermesData>)` `show(<RangedHermesData>)`	Show Method for `AnyHermesData` Objects
`subset`	Subsetting `AnyHermesData` Objects
`summary()` `show(<HermesDataSummary>)`	Summary Method for `AnyHermesData` Objects
Functions
`add_quality_flags()` `h_low_expression_flag()` `h_low_depth_flag()` `h_tech_failure_flag()` `get_tech_failure()` `get_low_depth()` `get_low_expression()`	Add Quality Flags
`calc_pca()`	Principal Components Analysis Calculation
`diff_expression()` `autoplot(<HermesDataDiffExpr>)`	Differential Expression Analysis
`set_tech_failure()`	Set Technical Failure Flags
`top_genes()` `autoplot(<HermesDataTopGenes>)`	Derivation of Top Genes
`connect_biomart()`	Connection to BioMart
`df_cols_to_factor()`	Conversion of Eligible Columns to Factor Variables in a `DataFrame`
`colPrinComp1()`	First Principal Component (PC1) Gene Signature
`colMeanZscores()`	Mean Z-score Gene Signature
`wrap_in_mae()`	Wrap in MAE
`col_data_with_genes()`	Sample Variables with Selected Gene Information
`inner_join_cdisc()`	Inner Joining a Genes with a CDISC Data Set
`cut_quantile()`	Cutting a Numeric Vector into a Factor of Quantile Bins
Graphs
`draw_libsize_hist()`	Histogram of Library Sizes
`draw_libsize_qq()`	Q-Q Plot of Library Sizes
`draw_libsize_densities()`	Density Plot of (Log) Counts Distributions
`draw_nonzero_boxplot()`	Boxplot of Non-Zero Genes
`draw_genes_barplot()`	Stacked Barplot of Low Expression Genes by Chromosome
`draw_scatterplot()`	Scatterplot for Gene Expression Values
`draw_barplot()`	Barplot for Gene Expression Percentiles
`draw_boxplot()` `h_draw_boxplot_df()`	Boxplot for Gene Expression Values
`autoplot(<AnyHermesData>)`	All Standard Plots in Default Setting
Control Functions
`control_normalize()`	Control Settings for Counts Normalization
`control_quality()`	Control for Specified Quality Flags
Assertions
`assertion_arguments`	Standard Assertion Arguments
`check_proportion()` `assert_proportion()` `test_proportion()` `expect_proportion()`	Check for proportion
`is_class()` `is_hermes_data()` `is_counts_vector()` `is_list_with()` `one_provided()` `is_constant()`	Additional Assertions for `assert_that`
Constants
`annotation(<AnyHermesData>)` `.row_data_annotation_cols` `annotation<-`(<AnyHermesData>,<DataFrame>)	Annotation Accessor and Setter

Reference

Package

Classes

Constructors

Internal Helper Functions

Example Data

Methods

Functions

Graphs

Control Functions

Assertions

Constants