PrepareAnnotationRefseq2: Prepare annotation from Refseq

In Shawn-Xu/PGA: An package for identification of novel peptides by customized database derived from RNA-Seq

Description

Prepare the annotation for Refseq through UCSC table browser. This function is modified from the function PrepareAnnotationRefseq in customProDB.

Usage

PrepareAnnotationRefseq2(genome = "hg19", CDSfasta, pepfasta, annotation_path,
  dbsnp = NULL, transcript_ids = NULL, splice_matrix = FALSE,
  COSMIC = FALSE, ...)

Arguments

genome	See detail in function PrepareAnnotationRefseq.
CDSfasta	See detail in function PrepareAnnotationRefseq.
pepfasta	See detail in function PrepareAnnotationRefseq.
annotation_path	See detail in function PrepareAnnotationRefseq.
dbsnp	See detail in function PrepareAnnotationRefseq.
transcript_ids	See detail in function PrepareAnnotationRefseq.
splice_matrix	See detail in function PrepareAnnotationRefseq.
COSMIC	See detail in function PrepareAnnotationRefseq.
...	Additional arguments

Value

Several .RData file containing annotations needed for following analysis.

See Also

PrepareAnnotationEnsembl2.

Examples

## Not run: 
transcript_ids <- c("NM_001126112", "NM_033360", "NR_073499")
pepfasta <- system.file("extdata", "refseq_pro_seq.fasta",
                        package="customProDB")
CDSfasta <- system.file("extdata", "refseq_coding_seq.fasta",
                        package="customProDB")
annotation_path <- tempdir()
PrepareAnnotationRefseq2(genome='hg19', CDSfasta, pepfasta, annotation_path,
                        dbsnp=NULL, transcript_ids=transcript_ids,
                        splice_matrix=FALSE, COSMIC=FALSE)

## End(Not run)

Shawn-Xu/PGA documentation built on Aug. 28, 2020, 9:58 p.m.