# Preprocessing, analyzing, and reporting of RNA-seq data

## Documentation for package ‘hermes’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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_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