Package index • hermes

Package

hermes 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_heatmap(): Heatmap for Gene Expression Counts

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