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

In chambm/customProDB: Generate customized protein databases from NGS 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 for calculating transcript FPKMs.
RPKM	Alternative to bamFile. If non-NULL, must be a vector containing expression level for proteins (e.g. FPKMs from cufflinks).
vcfFile	Input VCF file name.
annotation_path	The path to read annotation files from (e.g. ids.RData, exon_anno.RData, etc.).
outfile_path	Folder path for the output FASTA files.
outfile_name	Output FASTA file prefix.
rpkm_cutoff	The cutoff for RPKM values. See 'cutoff' in function Outputproseq for more detail.
INDEL	Set to TRUE to create a FASTA of the variations due to short insertions and deletions in the VCF (default is FALSE).
lablersid	Set to TRUE to include dbSNP rsid as a prefix to each SNP in the FASTA headers (default is FALSE). If TRUE, the annotation folder must have the dbsnpinCoding.RData file.
COSMIC	Set to TRUE to include COSMIC ids in the variation table (default is FALSE). If TRUE, the annotation folder must have the cosmic.RData file.
nov_junction	Set to TRUE to create a FASTA of the peptides that cover novel junctions. If TRUE, the annotation folder must have the splicemax.RData file, and the bedFile and genome parameters must be provided.
bedFile	Path to a .bed file which contains the splice junctions identified in RNA-Seq (e.g. junctions.bed from TopHat).
genome	A BSgenome object (e.g. BSgenome.Hsapiens.UCSC.hg19::Hsapiens). Default is NULL.
...	Additional arguments

Details

This function provides a convenient way to generate customized databases for a single sample based on transcript expression, SNV and INDEL variants, and novel junctions detected during RNA-Seq mapping.

Value

NULL. It creates several FASTA files in <outfile_path>; always creates <outfile_name>_rpkm.fasta and <outfile_name>_snv.fasta. Optionally creates <outfile_name>_indel.fasta and <outfile_name>_junc.fasta.

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)

chambm/customProDB documentation built on May 31, 2019, 12:08 p.m.