createProDB4DenovoRNASeq: Create protein database based on the transcripts from de novo...

In Shawn-Xu/PGA: An package for identification of novel peptides by customized database derived from RNA-Seq

Description

Create protein database based on the transcripts from de novo reconstruction of transcriptome from RNA-seq data.

Usage

createProDB4DenovoRNASeq(infa = "./trinity.fasta", bool_use_3frame = FALSE,
  outmtab = "novel_transcripts_ntx.tab",
  outfa = "./novel_transcripts_ntx.fasta", bool_get_longest = TRUE,
  make_decoy = TRUE, decoy_tag = "#REV#", outfile_name = "test")

Arguments

infa	A FASTA format file containing transcript sequences (such as derived from de novo transcriptome assembly by Trinity)
bool_use_3frame	A logical variable indicating whether to translate the raw sequences with 3-frame (forward). Default is 6-frame translation (FALSE).
outmtab	A txt format file containing the novel transcripts information
outfa	The output fasta format protein sequence file
bool_get_longest	When it's set as TRUE, only the longest protein sequences will be retained after the raw sequences are translated with 3-frame or 6-frame. Otherwise, all the protein sequences with longer than 30 aa will be retained.
make_decoy	A logical variable indicating whether to add the decoy sequences.
decoy_tag	The prefix of decoy sequence IDs.
outfile_name	Output file name

Value

The database file(s)

Examples

transcript_seq_file <- system.file("extdata/input", "Trinity.fasta",package="PGA")
createProDB4DenovoRNASeq(infa=transcript_seq_file)

Shawn-Xu/PGA documentation built on Aug. 28, 2020, 9:58 p.m.