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
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.
fasta2DNAbin(file, quiet=FALSE, chunkSize=10, snpOnly=FALSE)
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
a logical stating whether a conversion messages should be printed (FALSE, default) or not (TRUE).
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.
a logical indicating whether SNPs only should be returned.
an object of the class
Thibaut Jombart firstname.lastname@example.org
?DNAbin for a description of the class
read.snp: read SNPs in adegenet's '.snp' format.
read.PLINK: read SNPs in PLINK's '.raw' format.
df2genind: convert any multiallelic markers into
import2genind: read multiallelic markers from various
software into adegenet.
## 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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.