Man pages for DarwinAwardWinner/rctutils
Utility functions by Ryan C. Thompson
| add_bfdr | Add Bayesian FDR values to a limma top table |
| add_numbered_colnames | Add numbered colnames with a common prefix. |
| add_qvalue | Add a q-value column to any table with a p-value column |
| assign_into | Assign into complex sub-expressions and return the whole... |
| auto_factorize_columns | Intelligently convert character columns to factors in a data... |
| aveLogCPMWithOffset | Version of 'edgeR::aveLogCPM()' that uses offsets by default |
| bfdr | Compute Bayesian FDR values from limma's B-statistics |
| cairo_pdf_onefile | Same as 'cairo_pdf()' but with a default of 'onefile = TRUE' |
| cleanup_mcols | Remove valueless mcols from an object |
| code_control_named | Variant of code_control that generates more verbose column... |
| collapse_to_atomic | Convert a list to an atomic vector. |
| combineFCResults | Combine multiple featureCounts results |
| cpmWithOffset | Version of 'edgeR::cpm()' that uses offsets |
| deparse_onestring | Deparse and then concatenate into a single string |
| dot_mutate | Evaluate an arbitrary mutating expression in a magrittr pipe |
| eBayes_auto_proportion | Variant of 'limma::eBayes()' that sets the 'proportion'... |
| ensure_atomic_columns | Ensure that all columns of a data frame are atomic vectors. |
| estimateDispByGroup | Estimate edgeR dispersions separately for each group |
| fac2char | Convert all factors in a data frame to character vectors |
| featureCountsParallel | (Alternative) parallel version of 'Rsubread::featureCounts()' |
| featureCountsQuiet | 'Rsubread::featureCounts()' with output suppressed |
| first_accessible_path | Find the first accessible file path from a vector of paths. |
| format_bp | Format a number of base pairs using the most appropriate... |
| getBCVTable | Get a table of genewise BCV values from a DGEList |
| get_mds | Get a table of MDS values, with proper column names. |
| get_pval_colname | Determine the column name of the p-value column in a table |
| get_tx2gene_from_txdb | Generate a tx2gene table from a TxDb |
| get_txdb | Get a TxDb from either a package name or file name |
| ggduo_dataXY | Variant of 'GGally::ggduo()' with separate arguments for... |
| ggplotBCV | ggplot version of 'edgeR::plotBCV()'. |
| is_valueless | Determine whether a list or vector has any non-missing... |
| liftOverLax | Like 'rtracklayer::liftOver()' but "fills in" small gaps. |
| liftOver_motifMap | Convenience function for running liftOver on a MotifMap BED... |
| load_filtered | Variant of 'load()' that allows excluding specific names |
| load_in_new_env | Load an R data file into a new environment |
| make_futures | Construct futures for several expressions |
| make_futures_ | Construct futures for a list of expressions |
| match_arg | Improved match.arg with better errors and case folding. |
| mutate_if_present | Perform mutations only if specific column names are present |
| parse_bp | Parse a number of base pairs with optional units. |
| plot_pval_hist | Create an annotatied p-value histogram plot |
| print_var_vector | Print a readable summary of a list of values. |
| promote_common_mcols | Promote common mcols from the GRanges inside a GRangesList |
| quotemeta | Escape a string for use in a Perl-compatible regular... |
| rctutils-package | Common imports |
| read_motifmap | Read MotifMap-provided BED file into a GRanges object. |
| read_narrowPeak | Read a narrowPeak format BED file. |
| read_RDS_or_RDA | Read a single object from an RDS or RDA file |
| read_regions | Read a GRanges from a variety of possible file types. |
| read_saf | Read a SAF file into a GRangesList. |
| read_single_object_from_rda | Read a single R object from an RDA file. |
| readsToFragmentMidpoints | Compute the midpoints of a collection of read fragments |
| read_table_general | General function for reading a table from any table-like file |
| read_tx2gene_from_genemap | Read a Salmon "geneMap" file into a data frame |
| relevel_columns | Relevel many factor columns in a data frame at once |
| req_ns | Shortcut for the usual "requireNamespace" dance |
| save_image_filtered | Variant of 'save.image()' that allows excluding specific... |
| save_RDS_or_RDA | Save a single object to am RDS or RDA file |
| selectModelParallel | Parallelized version of 'limma::selectModel()' |
| si2f | Inverse of 'sitools::f2si()' |
| sprintf_single_value | Like 'sprintf()' but using the same value in each... |
| strip_design_factor_names | Simplify the column names of a simple design matrix |
| subtractCoefs | Alternative interface to 'limma::removeBatchEffect()' |
| tsmsg | Like 'message' but with a timestamp |
| voomWithDuplicateCorrelation | Alternate 'limma::duplicateCorrelation()' and 'limma::voom()'... |
| voomWithOffset | Implementation of 'limma::voom()' that uses an offset matrix |
| voomWithQualityWeightsAndOffset | Implementation of 'limma::voomWithQualityWeights()' that uses... |
| windowCountsParallel | Parallel version of 'csaw::windowCounts()' |
| with_gc | Evaluate an expression and then collect garbage. |
| write_motifmap | Write a MotifMap-type GRanges into a BED file. |
| write_narrowPeak | Write a narrowPeak format BED file. |
