easyRun: An integrated function to generate customized protein...

In customProDB: Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

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

Details

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

Value

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

Author(s)

Xiaojing Wang

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)

customProDB documentation built on Nov. 8, 2020, 8:06 p.m.