easyRun {customProDB} | R Documentation |
Generate a customized protein database for a single sample.
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, ...)
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 |
The function gives a more convenient way for proteomics researchers to generate customized database for a single sample.
A table file contains detailed variation information and several FASTA files.
Xiaojing Wang
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)