customProDB (version 1.12.0)

easyRun_mul: An integrated function to generate consensus protein database from multiple samples

Description

Generate consensus protein database for multiple samples in a single function.

Usage

easyRun_mul(bamFile_path, RPKM_mtx = NULL, vcfFile_path, annotation_path, rpkm_cutoff, share_num = 2, var_shar_num = 2, outfile_path, outfile_name, INDEL = FALSE, lablersid = FALSE, COSMIC = FALSE, nov_junction = FALSE, bedFile_path = NULL, genome = NULL, junc_shar_num = 2, ...)

Arguments

bamFile_path

The path of BAM files

RPKM_mtx

Alternative to bamFile_path,default NULL, a matrix containing expression level for proteins in each sample. (e.g. FPKMs from cufflinks)

vcfFile_path

The path of VCF files

annotation_path

The path of already saved annotation, which will be used in the function

rpkm_cutoff

Cutoffs of RPKM values. see 'cutoff' in function OutputsharedPro for more information

share_num

The minimum share sample numbers for proteins which pass the cutoff.

var_shar_num

Minimum sample number of recurrent variations.

outfile_path

The path of output FASTA file

outfile_name

The name prefix of output FASTA file

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_path

The path of BED files which contains the splice junctions identified in RNA-Seq.

genome

A BSgenome object(e.g. Hsapiens). Default is NULL. Required if nov_junction==TRUE.

junc_shar_num

Minimum sample number of recurrent splicing junctions.

...

Additional arguments

Value

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

Details

The function give a more convenient way for proteinomics researchers to generate customized database of multiple samples.

Examples

bampath <- system.file("extdata/bams", package="customProDB")
vcfFile_path <- system.file("extdata/vcfs", package="customProDB")
annotation_path <- system.file("extdata/refseq", package="customProDB")
outfile_path <- tempdir()
outfile_name <- 'mult'

easyRun_mul(bampath, RPKM_mtx=NULL, vcfFile_path, annotation_path, rpkm_cutoff=1,
            share_num=2, var_shar_num=2, outfile_path, outfile_name, INDEL=TRUE,
            lablersid=TRUE, COSMIC=TRUE, nov_junction=FALSE)