OutputNovelJun {customProDB} | R Documentation |
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.
OutputNovelJun(junction_type, genome, outfile, proteinseq, ...)
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. |
FASTA file that contains novel junction peptides.
Xiaojing Wang
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)