This function takes a proteome (in data.table notation) as returned by read.proteome and saves it to your hard drive.

write.proteome(proteome,, nbchar = 80, open = "w", as.string = TRUE)



a data.table object storing amino acid sequences in the first column and gene ids in the second column. See read.proteome for details.

a character string specifying the name of the fasta output file.


number of characters per line.


mode to open the output file, you can choose from "w" to write into a new file, or "a" to append at the end of an already existing file.


when set to TRUE sequences are in the form of strings instead of vectors of single characters.


if (FALSE) { # read an example proteome Ath.proteome <- read.proteome( system.file('seqs/ortho_thal_aa.fasta', package = 'orthologr'), format = "fasta") # use the write.proteome function to store it on your hard drive write.proteome(Ath.proteome, "test_proteome.fasta") }