easyRun_mul {customProDB} | R Documentation |
Generate consensus protein database for multiple samples in a single function.
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, ...)
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 |
The function give a more convenient way for proteinomics researchers to generate customized database of multiple samples.
A table file contains detailed variation information and several FASTA files.
Xiaojing Wang
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)