PrepareAnnotationRefseq2 {PGA} | R Documentation

## 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)

[Package PGA version 1.8.1 Index]