PrepareAnnotationRefseq2: Prepare annotation from Refseq

Description Usage Arguments Value See Also Examples

Description

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

Usage

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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

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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)


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