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

Description Usage Arguments Value Examples

Description

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

Usage

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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

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


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