scran.js
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Single cell RNA-seq analysis in Javascript
199 lines (180 loc) • 7.12 kB
JavaScript
import * as utils from "./utils.js";
/**
* Guess the identity of the features from their names.
*
* @param {Array} features - Array of strings containing feature identifiers, typically Ensembl IDs or gene symbols.
* Elements may also be `null` or undefined if an identifier is missing.
* @param {object} [options={}] - Optional parameters.
* @param {boolean} [options.forceTaxonomy=false] - Whether to force the use of taxonomy IDs for human and mouse.
* This is `false` for back compatibility.
*
* @return {object} An object containing:
*
* - `species`, the inferred species as a string.
* This can be either `"human"` or `"mouse"`, or an NCBI taxonomy ID (one of 6239, 10116, 9541, 7227, 7955, 9598).
* If `forceTaxonomy = true`, human and mouse are replaced with 9606 and 10090, respectively.
* - `type`: the feature identifier type.
* This can either be `"ensembl"` or `"symbol"`.
* - `confidence`: the percentage of entries in `x` that are consistent with the inferred identity.
*/
export function guessFeatures(features, options = {}) {
const { forceTaxonomy = false, ...others } = options;
utils.checkOtherOptions(others);
let ntotal = features.length;
let early_threshold = Math.ceil(ntotal / 2);
let format = payload => {
payload.confidence /= ntotal;
return payload;
};
// Duplicated entries only count as one match, so as to avoid problems with
// chromosome positions, feature type specifications, etc. Note that we
// still need to use the full length to compute 'ntotal', otherwise we
// wouldn't be penalizing the duplicates properly.
let unique_features = new Set;
for (const f of features) {
if (typeof f == "string") {
unique_features.add(f);
}
}
let ensembl_human = 0;
let ensembl_mouse = 0;
let ensembl_6239 = 0;
let ensembl_10116 = 0; // Ensembl only, Rat symbols are indistiguishable from mice.
let ensembl_9541 = 0; // Ensembl only, Mfac symbols are indistiguishable from human.
let ensembl_7227 = 0; // Ensembl only, fly symbols are crazy.
let ensembl_7955 = 0;
let ensembl_9598 = 0; // Ensembl only, Chimp symbols are indistinguishable from human.
let symbol_human = 0;
let symbol_mouse = 0;
let symbol_6239 = 0;
let symbol_7955 = 0;
let hsid = (forceTaxonomy ? "9606" : "human");
let mmid = (forceTaxonomy ? "10090" : "mouse");
let collected = [];
// Checking if it's any type of Ensembl.
let any_ens = 0;
for (const x of unique_features) {
if (x && x.match(/^ENS[A-Z]*G[0-9]{11}$/)) {
any_ens++;
}
}
if (any_ens) {
for (const x of unique_features) {
if (x) {
if (x.startsWith("ENSG")) {
ensembl_human++;
} else if (x.startsWith("ENSMUSG")) {
ensembl_mouse++;
} else if (x.startsWith("ENSRNOG")) {
ensembl_10116++;
} else if (x.startsWith("ENSMFAG")) {
ensembl_9541++;
} else if (x.startsWith("ENSDARG")) {
ensembl_7955++;
} else if (x.startsWith("ENSPTRG")) {
ensembl_9598++;
}
}
}
collected.push({ species: hsid, type: "ensembl", confidence: ensembl_human });
collected.push({ species: mmid, type: "ensembl", confidence: ensembl_mouse });
collected.push({ species: "10116", type: "ensembl", confidence: ensembl_10116 });
collected.push({ species: "9541", type: "ensembl", confidence: ensembl_9541 });
collected.push({ species: "7955", type: "ensembl", confidence: ensembl_7955 });
collected.push({ species: "9598", type: "ensembl", confidence: ensembl_9598 });
// See if we can quit early and avoid the other checks.
for (const x of collected) {
if (x.confidence >= early_threshold) {
return format(x);
}
}
}
// Human symbol; starts with upper case, no lower case, and not an Ensembl of any kind.
// We also ignore VEGA gene identifiers, as these are antiquated; and MGI identifiers,
// which are all-caps and thus confusing.
for (const x of unique_features) {
if (x && x.match(/^[A-Z][^a-z]+$/) && !x.match(/^ENS[A-Z]+[0-9]{11}/) && !x.match(/^OTT.{4}[0-9]{11}/) && !x.match(/^MGI:[0-9]+/)) {
symbol_human++;
}
}
{
let payload = { species: hsid, type: "symbol", confidence: symbol_human };
if (payload.confidence >= early_threshold) {
return format(payload);
}
collected.push(payload);
}
// Mouse symbol; starts with upper case, but no upper case after that.
for (const x of unique_features) {
if (x && x.match(/^[A-Z][^A-Z]+$/)) {
symbol_mouse++;
}
}
{
let payload = { species: mmid, type: "symbol", confidence: symbol_mouse };
if (payload.confidence >= early_threshold) {
return format(payload);
}
collected.push(payload);
}
// Worm Ensembl (WormBase).
for (const x of unique_features) {
if (x && x.match(/^WBGene[0-9]+$/)) {
ensembl_6239++;
}
}
{
let payload = { species: "6239", type: "ensembl", confidence: ensembl_6239 };
if (payload.confidence >= early_threshold) {
return format(payload);
}
collected.push(payload);
}
// Fly Ensembl (FlyBase).
for (const x of unique_features) {
if (x && x.match(/^FBgn[0-9]+$/)) {
ensembl_7227++;
}
}
{
let payload = { species: "7227", type: "ensembl", confidence: ensembl_7227 };
if (payload.confidence >= early_threshold) {
return format(payload);
}
collected.push(payload);
}
// Worm symbols; at least three lower case with a dash and numbers.
for (const x of unique_features) {
if (x && x.match(/^[a-z]{3,}-[0-9]+$/)) {
symbol_6239++;
}
}
{
let payload = { species: "6239", type: "symbol", confidence: symbol_6239 };
if (payload.confidence >= early_threshold) {
return format(payload);
}
collected.push(payload);
}
// Zebrafish symbols; at least three lower case letters, no dash, followed by numbers and/or more lower case.
for (const x of unique_features) {
if (x && x.match(/^[a-z]{3,}[0-9a-z]+$/)) {
symbol_7955++;
}
}
{
let payload = { species: "7955", type: "symbol", confidence: symbol_7955 };
if (payload.confidence >= early_threshold) {
return format(payload);
}
collected.push(payload);
}
// Picking the best.
let highest = collected[0];
for (var i = 1; i < collected.length; i++) {
if (collected[i].confidence > highest.confidence) {
highest = collected[i];
}
}
return format(highest);
}