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Package index

Package

hermes hermes-package
hermes Package

Classes

HermesData() HermesDataFromMatrix() experimental
HermesData and RangedHermesData
correlate(<AnyHermesData>) autoplot(<HermesDataCor>) experimental
Correlation between Sample Counts of AnyHermesData
calc_pca() experimental
Principal Components Analysis Calculation
top_genes() autoplot(<HermesDataTopGenes>) experimental
Derivation of Top Genes
summary() show(<HermesDataSummary>) experimental
Summary Method for AnyHermesData Objects
correlate(<HermesDataPca>) autoplot(<HermesDataPcaCor>) stable
Correlation of Principal Components with Sample Variables
diff_expression() autoplot(<HermesDataDiffExpr>) experimental
Differential Expression Analysis
connect_biomart() experimental
Connection to BioMart
GeneSpec experimental
R6 Class Representing a Gene (Signature) Specification

Constructors

HermesData() HermesDataFromMatrix() experimental
HermesData and RangedHermesData
gene_spec() experimental
GeneSpec Constructor

Internal Helper Functions

all_na()
Checks Whether All Missing
cat_with_newline() experimental
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() stable
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() stable
Add Quality Flags
h_diff_expr_voom() experimental
limma/voom Differential Expression Analysis
h_diff_expr_deseq2() experimental
DESeq2 Differential Expression Analysis
h_pca_var_rsquared() stable
Calculation of R2 between Sample Variable and Principal Components
h_pca_df_r2_matrix() stable
Calculation of R2 Matrix between Sample Variables and Principal Components
h_get_annotation_biomart() experimental
Get Annotations from BioMart
h_get_granges_by_id() experimental
Conversion of BioMart Coordinates into GRanges
h_get_size_biomart() experimental
Total Length of All Exons for Genes
h_ensembl_to_entrez_ids() experimental
Translation of Ensembl to Entrez Gene IDs
h_strip_prefix() experimental
Stripping Prefix from Gene IDs
h_has_req_annotations() experimental
Predicate for Required Annotations
h_short_list() experimental
Make a Short List of a Character Vector
h_parens() experimental
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() experimental
Conversion to Factors with Explicit Missing Level in a data.frame
draw_boxplot() h_draw_boxplot_df() experimental
Boxplot for Gene Expression Values

Example Data

expression_set stable
Example ExpressionSet Data
hermes_data stable
Example HermesData Data
summarized_experiment stable
Example SummarizedExperiment Data
multi_assay_experiment experimental
Example MultiAssayExperiment Data

Methods

annotation(<AnyHermesData>) .row_data_annotation_cols `annotation<-`(<AnyHermesData>,<DataFrame>) stable
Annotation Accessor and Setter
cbind stable
Column Binding of AnyHermesData Objects
correlate() experimental
Generic Function for Correlation Calculations
counts(<AnyHermesData>) `counts<-`(<AnyHermesData>,<matrix>) stable
Counts Accessor and Setter
extraColDataNames() extraRowDataNames() experimental
Extra Variable Names Accessor Methods
filter() stable
Filter AnyHermesData on Subset Passing Default QC Flags
genes() stable
Gene IDs Accessor
isEmpty(<SummarizedExperiment>) experimental
Checking for Empty SummarizedExperiment
lapply(<MultiAssayExperiment>) experimental
lapply method for MultiAssayExperiment
metadata stable
Metadata Accessor and Setter
normalize(<AnyHermesData>) h_cpm() h_rpkm() h_tpm() h_voom() h_vst() h_rlog() stable
Normalization of AnyHermesData Objects
prefix() experimental
Prefix Accessor
query() experimental
Query Gene Annotations from a Connection
rbind stable
Row Binding of AnyHermesData Objects
rename(<SummarizedExperiment>) rename(<data.frame>) experimental
Renaming Contents of SummarizedExperiment Objects
samples(<AnyHermesData>) stable
Sample IDs Accessor
show(<HermesData>) show(<RangedHermesData>) experimental
Show Method for AnyHermesData Objects
subset stable
Subsetting AnyHermesData Objects
summary() show(<HermesDataSummary>) experimental
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() stable
Add Quality Flags
calc_pca() experimental
Principal Components Analysis Calculation
diff_expression() autoplot(<HermesDataDiffExpr>) experimental
Differential Expression Analysis
set_tech_failure() experimental
Set Technical Failure Flags
top_genes() autoplot(<HermesDataTopGenes>) experimental
Derivation of Top Genes
connect_biomart() experimental
Connection to BioMart
df_cols_to_factor() experimental
Conversion of Eligible Columns to Factor Variables in a DataFrame
colPrinComp1() experimental
First Principal Component (PC1) Gene Signature
colMeanZscores() experimental
Mean Z-score Gene Signature
wrap_in_mae() experimental
Wrap in MAE
col_data_with_genes() experimental
Sample Variables with Selected Gene Information
inner_join_cdisc() experimental
Inner Joining a Genes with a CDISC Data Set
cut_quantile() experimental
Cutting a Numeric Vector into a Factor of Quantile Bins

Graphs

draw_libsize_hist() experimental
Histogram of Library Sizes
draw_libsize_qq() experimental
Q-Q Plot of Library Sizes
draw_libsize_densities() experimental
Density Plot of (Log) Counts Distributions
draw_nonzero_boxplot() experimental
Boxplot of Non-Zero Genes
draw_genes_barplot() experimental
Stacked Barplot of Low Expression Genes by Chromosome
draw_heatmap() experimental
Heatmap for Gene Expression Counts
draw_scatterplot() experimental
Scatterplot for Gene Expression Values
draw_barplot() experimental
Barplot for Gene Expression Percentiles
draw_boxplot() h_draw_boxplot_df() experimental
Boxplot for Gene Expression Values
autoplot(<AnyHermesData>) experimental
All Standard Plots in Default Setting

Control Functions

control_normalize() stable
Control Settings for Counts Normalization
control_quality() stable
Control for Specified Quality Flags

Assertions

assertion_arguments
Standard Assertion Arguments
check_proportion() assert_proportion() test_proportion() expect_proportion() experimental
Check for proportion
is_class() is_hermes_data() is_counts_vector() is_list_with() one_provided() is_constant() experimental
Additional Assertions for assert_that

Constants

annotation(<AnyHermesData>) .row_data_annotation_cols `annotation<-`(<AnyHermesData>,<DataFrame>) stable
Annotation Accessor and Setter