PrepareAnnotationRefseq2: Prepare annotation from Refseq

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

Prepare annotation from Refseq

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)

wenbostar/PGA documentation built on March 24, 2022, 6:48 p.m.