Namespace: userData

userData

Source:

Methods

(async, static) convertMatrix(data, group_byopt, batch_sizeopt, genomeopt, tcgaopt) → {Promise.<Object>}

Converts input mutational data into a mutational spectrum matrix grouped by a specified field. This function processes raw mutational data, extracts trinucleotide contexts, and aggregates mutational spectra for each group. It supports TCGA and non-TCGA formats, allowing batch processing for large datasets. The resulting mutational spectrum matrix is formatted for downstream visualization and analysis.
Parameters:
Name Type Attributes Default Description
data Array.<Array.<Object>> Array of patient-level mutational data. Each patient's data is represented as an array of objects, where each object contains mutational details (e.g., chromosome, position, mutation type).
group_by string <optional>
 "Center" Field to group data by (e.g., "Center" or "sample_id"). This field should exist in the input data.
batch_size number <optional>
 100 Number of mutations to process in parallel batches. Adjust this for memory management.
genome string <optional>
 "hg19" Reference genome build. Defaults to "hg19" unless specified in the data.
tcga boolean <optional>
 false Flag indicating whether the input data is in TCGA format. If true, expects TCGA-specific fields.
Source:
Returns:
- A promise resolving to an object where each key is a group (e.g., "CNIC"), and each value is a mutational spectrum object. The mutational spectrum object contains trinucleotide contexts as keys (e.g., "A[C>A]A") and counts as values.
Type
Promise.<Object>
Example
// Example input data
const data = [
  [
    { chromosome: "1", start_position: "12345", reference_allele: "C", tumor_seq_allele2: "T", variant_type: "SNP", build: "hg19", Center: "CNIC" },
    { chromosome: "2", start_position: "67890", reference_allele: "G", tumor_seq_allele2: "A", variant_type: "SNP", build: "hg19", Center: "CNIC" }
  ],
  [
    { chromosome: "3", start_position: "101112", reference_allele: "T", tumor_seq_allele2: "C", variant_type: "SNP", build: "hg19", Center: "OtherCenter" }
  ]
];

// Convert data to mutational spectra grouped by Center
const mutationalSpectra = await convertMatrix(data, "Center", 50, "hg19", false);
console.log(mutationalSpectra);
// Output:
// {
//   "CNIC": {
//     "A[C>A]A": 9,
//     "A[C>A]C": 7,
//     "A[C>A]G": 6,
//     ...
//   },
//   "OtherCenter": {
//     "T[T>C]A": 15,
//     "T[T>C]T": 8,
//     ...
//   }
// }

(static) convertMutationalSpectraIntoJSON(MAFfiles, mutSpec, sample_name, dataTypeopt) → {Array}

Converts mutational spectra into JSON objects for downstream processing or storage. This function takes mutation annotation format (MAF) files, mutational spectra data, and sample names, and outputs JSON objects representing the spectra in a structured format.
Parameters:
Name Type Attributes Default Description
MAFfiles Array An array of arrays containing mutation annotation data for each sample. Each inner array represents a sample's mutation data, where each entry is an object with key-value pairs.
mutSpec Object An object representing the mutational spectra. Keys are patient identifiers, and values are objects with mutation types as keys and counts as values.
sample_name string The key in MAFfiles to be used as the sample identifier.
dataType string <optional>
 "WGS" The sequencing strategy, e.g., "WGS" (Whole Genome Sequencing) or "WES" (Whole Exome Sequencing).
Source:
Throws:
- If the number of MAF files and the number of mutational spectra do not match.
Type
Error
Returns:
- An array of arrays, where each inner array represents the JSON objects for a patient's mutational spectra.
Type
Array
Examples
// Example input:
const MAFfiles = [
  [{ sample_id: "Sample1", ch   mosome: "1", start_position: "12345", ... }],
  [{ sample_id: "Sample2", ch   mosome: "2", start_position: "67890", ... }]
];
const mutSpec = {
  Patient1: { "A[C>A]A": 10,    [C>A]C": 5, "A[C>A]G": 8, ... },
  Patient2: { "A[C>A]A": 7, "   C>A]C": 4, "A[C>A]G": 6, ... }
};
const sample_name = "sample_id";
const result = convertMutationalSpectraIntoJSON(MAFfiles, mutSpec, sample_name, "WES");
console.log(result);
// Example output:
[
  [
    { sample: "Sample1", strategy: "WES", profile: "SBS", matrix: 96, mutationType: "C>A", mutations: 10 },
    { sample: "Sample1", strategy: "WES", profile: "SBS", matrix: 96, mutationType: "C>G", mutations: 5 },
    ...
  ],
  [
    { sample: "Sample2", strategy: "WES", profile: "SBS", matrix: 96, mutationType: "C>A", mutations: 7 },
    { sample: "Sample2", strategy: "WES", profile: "SBS", matrix: 96, mutationType: "C>G", mutations: 4 },
    ...
  ]
];

(async, static) convertWGStoPanel(WgMAFs, panelDf) → {Array}

Converts Whole Genome Sequencing (WGS) mutation data into panel data by downsampling based on a BED file. This function takes WGS mutation annotation files (MAFs) and a BED file defining panel regions, then filters the WGS data to include only mutations within the specified panel regions.
Parameters:
Name Type Description
WgMAFs Array An array of WGS mutation data, where each element is an array representing mutations for a single sample. Each mutation record should be an object with fields such as `chromosome`, `start_position`, etc.
panelDf string | Array A BED file defining the regions of the panel or an array of arrays representing the panel regions. If a string is provided, it is treated as a file path to a BED file and read into memory.
Source:
Returns:
- An array of downsampled MAFs, where each element corresponds to a sample from the input WGS data, filtered to include only mutations within the panel regions.
Type
Array
Example
// Example input:
const WgMAFs = [
  [
    { chromosome: "1", start_position: 12345, Hugo_Symbol: "TP53", ... },
    { chromosome: "2", start_position: 67890, Hugo_Symbol: "BRCA1", ... },
    ...
  ],
  [
    { chromosome: "1", start_position: 54321, Hugo_Symbol: "KRAS", ... },
    { chromosome: "2", start_position: 98765, Hugo_Symbol: "EGFR", ... },
    ...
  ],
];
const panelDf = "panel_regions.bed"; // Path to a BED file.

// Convert WGS data to panel data
const panelMAFs = await convertWGStoPanel(WgMAFs, panelDf);

// Example output:
// panelMAFs = [
//   [
//     { chromosome: "1", start_position: 12345, Hugo_Symbol: "TP53", ... },
//     ...
//   ],
//   [
//     { chromosome: "2", start_position: 98765, Hugo_Symbol: "EGFR", ... },
//     ...
//   ]
// ];