fasta2genlight | R Documentation |
The function fasta2genlight
reads alignments with the fasta
format (extensions ".fasta", ".fas", or ".fa"), extracts the binary
SNPs, and converts the output into a genlight object.
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.
Multiple cores can be used to decrease the overall computational time
on parallel architectures (needs the package parallel
).
fasta2genlight(file, quiet = FALSE, chunkSize = 1000, saveNbAlleles = FALSE, parallel = FALSE, n.cores = NULL, ...)
file |
a character string giving the path to the file to convert, with the extension ".fa", ".fas", or ".fasta". |
quiet |
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. |
saveNbAlleles |
a logical indicating whether the number of
alleles for each loci in the original alignment should be saved in the
|
parallel |
a logical indicating whether multiple cores -if
available- should be used for the computations (TRUE, default), or
not (FALSE); requires the package |
n.cores |
if |
... |
other arguments to be passed to other functions - currently not used. |
=== Using multiple cores ===
Most recent machines have one or several processors with multiple
cores. R processes usually use one single core. The package
parallel
allows for parallelizing some computations on
multiple cores, which decreases drastically computational time.
To use this functionality, you need to have the last version of the
parallel
package installed.
an object of the class genlight
Thibaut Jombart t.jombart@imperial.ac.uk
- ?genlight
for a description of the class genlight.
- 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.
## 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 <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time obj ## look at extracted information position(obj) alleles(obj) locNames(obj) ## plot positions of polymorphic sites temp <- density(position(obj), bw=10) plot(temp, xlab="Position in the alignment", lwd=2, main="Location of the SNPs") points(position(obj), rep(0, nLoc(obj)), pch="|", col="red") ## End(Not run)
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