customProDB (version 1.12.0)

OutputNovelJun: generate peptide FASTA file that contains novel junctions.

Description

Three-frame translation of novel junctions. And remove those could be found in normal protein sequences. This function requires a genome built by BSgenome package.

Usage

OutputNovelJun(junction_type, genome, outfile, proteinseq, ...)

Arguments

junction_type

a data frame which is the output of function JunctionType()

genome

a BSgenome object. (e.g. Hsapiens)

outfile

output file name

proteinseq

a data frame cotaining amino acid sequence for each protein.

...

Additional arguments.

Value

FASTA file that contains novel junction peptides.

Examples

bedfile <- system.file("extdata/beds", "junctions1.bed", package="customProDB")
jun <-  Bed2Range(bedfile,skip=1,covfilter=5)
load(system.file("extdata/refseq", "splicemax.RData", package="customProDB"))
load(system.file("extdata/refseq", "ids.RData", package="customProDB"))
txdb <- loadDb(system.file("extdata/refseq", "txdb.sqlite",
            package="customProDB"))
junction_type <- JunctionType(jun, splicemax, txdb, ids)
table(junction_type[, 'jun_type'])
chrom <- paste('chr',c(1:22,'X','Y','M'),sep='')
junction_type <- subset(junction_type, seqnames %in% chrom)
outf_junc <- paste(tempdir(), '/test_junc.fasta', sep='')
load(system.file("extdata/refseq", "proseq.RData", package="customProDB"))
library('BSgenome.Hsapiens.UCSC.hg19')
OutputNovelJun <- OutputNovelJun(junction_type, Hsapiens, outf_junc,
            proteinseq)