Man pages for jmw86069/platjam
Platform Jam, biological platform importers.
| apply_word_wrap | Apply word-wrap to text, recognizing whitespace and some... |
| applyXlsxConditionalFormatByColumn | Apply Xlsx Conditional Formatting by Column |
| assign_numeric_colors | Assign color function to a numeric vector |
| assign_track_defaults | Assign default UCSC track values to environment |
| cardinality | Determine cardinality between two vectors |
| color_complement | Create color complement by rotating the color hue |
| convert_imputed_assays_to_na | Convert imputed metabolomics assay data to NA |
| convert_PD_df_to_SE | Internal function to convert Proteomics Discoverer data.frame... |
| coverage_matrix2nmat | Import genome coverage matrix files |
| curate_se_colData | Curate Summarized Experiment colData |
| curate_to_df_by_pattern | Curate vector to data.frame by pattern matching |
| deepTools_matrix2nmat | Import deepTools coverage matrix to normalizedMatrix |
| design2colors | Convert experiment design into categorical colors |
| design2layout | Convert experiment design into reasonable plot panel layout |
| df_to_numcolors | Convert data.frame to numeric color substitution |
| frequency_matrix2nmat | Convert frequency matrix to normalizedMatrix format |
| get_nmat_ceiling | Helper function to calculate signal ceiling of numeric matrix |
| get_numeric_transform | Get appropriate numeric transformation function |
| get_salmon_meta | Get Salmon metadata and aux info into a data.frame |
| get_salmon_root | Get Salmon root directory |
| get_track_defaults | Get UCSC track default values and track templates |
| handle_df_args | Handle function arguments passed in the form of a data.frame |
| import_lipotype_csv | Import LipoType lipidomics data from CSV file |
| import_metabolomics_niehs | Import metabolomics data from NIEHS file formats |
| import_nanostring_csv | Import Nanostring csv file |
| import_nanostring_rcc | Import Nanostring RCC files |
| import_nanostring_rlf | Import Nanostring RLF file for a codeset |
| import_omics_data | Import generic omics tsv or csv file |
| import_proteomics_mascot | Import proteomics data from Mascot |
| import_proteomics_PD | Import data from Proteomics Discoverer |
| import_salmon_quant | Import Salmon quant.sf files to SummarizedExperiment |
| make_ucsc_trackname | Make valid UCSC track name from character string |
| mean_hue | Mean hue for a vector |
| merge_proteomics_se | merge proteomics SE objects |
| nmathm_row_order | Make coverage heatmaps |
| nmatlist2heatmaps | Make multiple coverage heatmaps |
| nmatlist_summary | Quick summary of a list of normalizedMatrix data |
| nmat_summary | Quick summary of normalizedMatrix data |
| parse_salmon_flenfile | Parse Salmon fragment length file |
| parse_ucsc_gokey | Parse UCSC tracks that use the Gokey format |
| print_color_list | Print color list of color vectors or color functions |
| process_metab_compounds_file | Process NIEHS compounds output files (internal) |
| quick_complement_color | Quick color complement function |
| recenter_nmatlist | Re-center coverage matrix data |
| restrand_nmatlist | Re-strand coverage matrix data by inferred strandedness |
| rmd_tab_iterator | RMarkdown tab iterator |
| rowNormScale | Normalize and scale data per row |
| save_salmon_qc_xlsx | Save Salmon QC to Xlsx |
| summit_from_vector | Determine summit from numeric vector |
| validate_heatmap_params | Validate coverage heatmap params for Rmarkdown |
| zoom_nmat | Zoom the x-axis range for a normalizedMatrix coverage data |
| zoom_nmatlist | Zoom the x-axis range for a list of normalizedMatrix coverage... |
