write.fasta {vcfR} | R Documentation |
Create fasta format output
Description
Generate fasta format output
Usage
write.fasta(
x,
file = "",
rowlength = 80,
tolower = TRUE,
verbose = TRUE,
APPEND = FALSE,
depr = TRUE
)
Arguments
x |
object of class chromR |
file |
name for output file |
rowlength |
number of characters each row should not exceed |
tolower |
convert all characters to lowercase (T/F) |
verbose |
should verbose output be generated (T/F) |
APPEND |
should data be appended to an existing file (T/F) |
depr |
logical (T/F), this function has been deprecated, set to FALSE to override. |
Details
The function write_fasta takes an object of class chromR and writes it to a fasta.gz (gzipped text) format file. The sequence in the seq slot of the chromR object is used to fill in the invariant sites. The parameter 'tolower', when set to TRUE, converts all the characters in teh sequence to lower case. This is important because some software, such as ape::DNAbin, requires sequences to be in lower case.
[Package vcfR version 1.15.0 Index]