FeatureReader

Class for reading gene/protein information.

Access

const reader = await CloupeReader.open(file);
const featureReader = reader.features;

Properties

count

get count(): number

Returns the total number of features.

Methods

read()

async read(options?: PaginationOptions): Promise<Feature[]>

Reads feature list.

Returns

interface Feature {
  index: number; // Index in matrix
  id: string; // Ensembl ID, etc. (e.g., ENSG00000167286)
  name: string; // Gene symbol (e.g., CD3D)
  type?: string; // Feature type (e.g., Gene Expression)
}

Examples

// Read all
const features = await reader.features.read();
console.log(features[0]);
// { index: 0, id: "ENSG00000167286", name: "CD3D", type: "Gene Expression" }

// With pagination
const page = await reader.features.read({ offset: 0, limit: 100 });

readOne()

async readOne(index: number): Promise<Feature>

Reads a single feature.

search()

async search(query: string): Promise<Array<{ index: number; feature: Feature }>>

Searches features by name or ID. Case-insensitive.

Examples

// Search for genes starting with CD3
const results = await reader.features.search("CD3");

for (const { index, feature } of results) {
  console.log(`${feature.name} (${feature.id}) at index ${index}`);
}
// CD3D (ENSG00000167286) at index 1234
// CD3E (ENSG00000198851) at index 1235
// CD3G (ENSG00000160654) at index 1236

findByName()

async findByName(name: string): Promise<{ index: number; feature: Feature } | null>

Finds a feature by exact name. Case-insensitive.

Examples

const result = await reader.features.findByName("CD3D");

if (result) {
  console.log(`Found at index ${result.index}`);
  console.log(result.feature);
} else {
  console.log("Not found");
}

clearCache()

clearCache(): void

Clears cached data.

Feature Types

Common feature types:

Type	Description
Gene Expression	mRNA expression
Antibody Capture	CITE-seq proteins
CRISPR Guide Capture	Perturb-seq gRNAs
Multiplexing Capture	Cell hashing