PGA (version 1.2.2)

PrepareAnnotationRefseq2: 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

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)