A C D E F G H I L M N O P Q R S T V W misc
hermes-package | 'hermes' Package |
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 |
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 |
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 |
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 |
filter | Filter 'AnyHermesData' on Subset Passing Default QC Flags |
filter-method | Filter 'AnyHermesData' on Subset Passing Default QC Flags |
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 |
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 |
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' |
lapply | 'lapply' method for 'MultiAssayExperiment' |
lapply-method | 'lapply' method for 'MultiAssayExperiment' |
metadata | Metadata Accessor and Setter |
multi_assay_experiment | Example 'MultiAssayExperiment' Data |
normalize | Normalization of 'AnyHermesData' Objects |
normalize-method | Normalization of 'AnyHermesData' Objects |
one_provided | Additional Assertions for 'assert_that' |
pca_cor_samplevar | Correlation of Principal Components with Sample Variables |
plot_all | All Standard Plots in Default Setting |
prefix | Prefix Accessor |
query | Query Gene Annotations from a Connection |
query-method | Query Gene Annotations from a Connection |
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 |
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 |
test_proportion | Check for proportion |
top_genes | Derivation of Top Genes |
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 |
wrap_in_mae | Wrap in MAE |
.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 |