customProDB (version 1.12.0)

easyRun: An integrated function to generate customized protein database for a single sample

Description

Generate a customized protein database for a single sample.

Usage

easyRun(bamFile, RPKM = NULL, vcfFile, annotation_path, outfile_path, outfile_name, rpkm_cutoff = 1, INDEL = FALSE, lablersid = FALSE, COSMIC = FALSE, nov_junction = FALSE, bedFile = NULL, genome = NULL, ...)

Arguments

bamFile

Input BAM file name

RPKM

Alternative to bamFile,default NULL, a vector containing expression level for proteins. (e.g. FPKMs from cufflinks)

vcfFile

Input VCF file name.

outfile_path

Folder path for the output FASTA files.

outfile_name

Output FASTA file name.

annotation_path

The path of saved annotation.

rpkm_cutoff

The cutoff of RPKM value. see 'cutoff' in function Outputproseq for more detail.

INDEL

If the vcfFile contains the short insertion/deletion. Default is FALSE.

lablersid

If includes the dbSNP rsid in the header of each sequence, default is FALSE. Users should provide dbSNP information when running function Positionincoding() if put TRUE here.

COSMIC

If output the cosmic ids in the variation table.Default is FALSE. If choose TRUE, there must have cosmic.RData in the annotation folder.

nov_junction

If output the peptides that cover novel junction into the database. if TRUE, there should be splicemax.RData in the annotation folder.

bedFile

The path of bed file which contains the splice junctions identified in RNA-Seq.

genome

A BSgenome object(e.g. Hsapiens). Default is NULL.

...

Additional arguments

Value

A table file contains detailed variation information and several FASTA files.

Details

The function gives a more convenient way for proteomics researchers to generate customized database for a single sample.

Examples

bamFile <- system.file("extdata/bams", "test1_sort.bam",
            package="customProDB")
vcffile <- system.file("extdata/vcfs", "test1.vcf", package="customProDB")
annotation_path <- system.file("extdata/refseq", package="customProDB")
outfile_path <- tempdir()
outfile_name <- 'test'

easyRun(bamFile, RPKM=NULL, vcffile, annotation_path, outfile_path,
        outfile_name, rpkm_cutoff=1, INDEL=TRUE, lablersid=TRUE,
        COSMIC=TRUE, nov_junction=FALSE)