Function reference • platjam

Import functions Import functions
`coverage_matrix2nmat()`	Import genome coverage matrix files
`deepTools_matrix2nmat()`	Import deepTools coverage matrix to normalizedMatrix
`frequency_matrix2nmat()`	Convert frequency matrix to normalizedMatrix format
`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_proteomics_PD()`	Import data from Proteomics Discoverer
`import_proteomics_mascot()`	Import proteomics data from Mascot
`import_salmon_quant()`	Import Salmon quant.sf files to SummarizedExperiment
`process_metab_compounds_file()`	Process NIEHS compounds output files (internal)
Coverage heatmap functions Coverage heatmap functions
`coverage_matrix2nmat()`	Import genome coverage matrix files
`get_nmat_ceiling()`	Helper function to calculate signal ceiling of numeric matrix
`nmathm_row_order()`	Make coverage heatmaps
`nmatlist2heatmaps()`	Make multiple coverage heatmaps
`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 data
Jam color functions color manipulation and assignment
`assign_numeric_colors()`	Assign color function to a numeric vector
`design2colors()`	Convert experiment design into categorical colors
`df_to_numcolors()`	Convert data.frame to numeric color substitution
`mean_hue()`	Mean hue for a vector
`print_color_list()`	Print color list of color vectors or color functions
`quick_complement_color()`	Quick color complement function
UCSC genome browser track functions Functions related to the UCSC genome browser
`assign_track_defaults()`	Assign default UCSC track values to environment
`get_track_defaults()`	Get UCSC track default values and track templates
`make_ucsc_trackname()`	Make valid UCSC track name from character string
`parse_ucsc_gokey()`	Parse UCSC tracks that use the Gokey format
Nextgen sequence functions Functions related to the nextgen sequence data
`get_salmon_meta()`	Get Salmon metadata and aux info into a data.frame
`get_salmon_root()`	Get Salmon root directory
`parse_salmon_flenfile()`	Parse Salmon fragment length file
`save_salmon_qc_xlsx()`	Save Salmon QC to Xlsx
Utility functions Extra utility functions
`cardinality()`	Determine cardinality between two vectors
`color_complement()`	Create color complement by rotating the color hue
`convert_PD_df_to_SE()`	Internal function to convert Proteomics Discoverer data.frame to SummarizedExperiment
`convert_imputed_assays_to_na()`	Convert imputed metabolomics assay data to NA
`curate_se_colData()`	Curate Summarized Experiment colData
`curate_to_df_by_pattern()`	Curate vector to data.frame by pattern matching
`design2layout()`	Convert experiment design into reasonable plot panel layout
`get_numeric_transform()`	Get appropriate numeric transformation function
`handle_df_args()`	Handle function arguments passed in the form of a data.frame
`merge_proteomics_se()`	merge proteomics SE objects
`rowNormScale()`	Normalize and scale data per row
Export functions Data export functions
`applyXlsxConditionalFormatByColumn()`	Apply Xlsx Conditional Formatting by Column

Reference

Import functions

Coverage heatmap functions

Jam color functions

UCSC genome browser track functions

Nextgen sequence functions

Utility functions

Export functions