R: Read large DNA alignments into R

fasta2DNAbin {adegenet} | R Documentation

## Read large DNA alignments into R

### Description

The function `fasta2DNAbin` reads alignments with the fasta format (extensions ".fasta", ".fas", or ".fa"), and outputs a `DNAbin` object (the efficient DNA representation from the ape package). The output contains either the full alignments, or only SNPs. This implementation is designed for memory-efficiency, and can read in larger datasets than Ape's `read.dna`.

The function reads data by chunks of a few genomes (minimum 1, no maximum) at a time, which allows one to read massive datasets with negligible RAM requirements (albeit at a cost of computational time). The argument `chunkSize` indicates the number of genomes read at a time. Increasing this value decreases the computational time required to read data in, while increasing memory requirements.

### Usage

    fasta2DNAbin(file, quiet=FALSE, chunkSize=10, snpOnly=FALSE)

### Arguments

`file` | a character string giving the path to the file to convert, with the extension ".fa", ".fas", or ".fasta". Can also be a connection (which will be opened for reading if necessary, and if so `close`d (and hence destroyed) at the end of the function call).
`quiet` | a logical stating whether a conversion messages should be printed (FALSE, default) or not (TRUE).
`chunkSize` | an integer indicating the number of genomes to be read at a time; larger values require more RAM but decrease the time needed to read the data.
`snpOnly` | a logical indicating whether SNPs only should be returned.

### Value

an object of the class `DNAbin`

### Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

### See Also

- `?DNAbin` for a description of the class `DNAbin`.

- `read.snp`: read SNPs in adegenet's '.snp' format.

- `read.PLINK`: read SNPs in PLINK's '.raw' format.

- `df2genind`: convert any multiallelic markers into adegenet genind.

- `import2genind`: read multiallelic markers from various software into adegenet.

### Examples

    ## Not run:
    ## show the example file ##
    ## this is the path to the file:
    myPath <- system.file("files/usflu.fasta",package="adegenet")
    myPath

    ## read the file
    obj <- fasta2DNAbin(myPath, chunk=10) # process 10 sequences at a time
    obj

    ## End(Not run)

[Package adegenet version 2.1.4 Index]