encodeSequences {DropletUtils} | R Documentation

## Encode nucleotide sequences

### Description

Encode short nucleotide sequences into integers with a 2-bit encoding.

### Usage

    encodeSequences(sequences)

### Arguments

`sequences` | A character vector of short nucleotide sequences, e.g., UMIs or cell barcodes.

### Details

Each pair of bits encodes a nucleotide - 00 is A, 01 is C, 10 is G and 11 is T. The least significant byte contains the 3'-most nucleotides, and the remaining bits are set to zero. Thus, the sequence “CGGACT” is converted to the binary form:

        01 10 10 00 01 11

... which corresponds to the integer 1671.

A consequence of R's use of 32-bit integers means that no element of `sequences` can be more than 15 nt long. Otherwise, integer overflow will occur.

### Value

An integer vector containing the encoded sequences.

### Author(s)

Aaron Lun

### References

10X Genomics (2017). Molecule info. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/molecule_info

### Examples

    encodeSequences("CGGACT")

[Package DropletUtils version 1.12.3 Index]