PrepareAnnotationRefseq {customProDB} | R Documentation |
prepare the annotation for Refseq through UCSC table browser.
PrepareAnnotationRefseq(genome = "hg19", CDSfasta, pepfasta, annotation_path, dbsnp = NULL, transcript_ids = NULL, splice_matrix = FALSE, ClinVar = FALSE, ...)
genome |
specify the UCSC DB identifier (e.g. "hg19") |
CDSfasta |
path to the fasta file of coding sequence. |
pepfasta |
path to the fasta file of protein sequence, check 'introduction' for more detail. |
annotation_path |
specify a folder to store all the annotations. |
dbsnp |
specify a snp dataset to be used for the SNP annotation, default is NULL. (e.g. "snp148") |
transcript_ids |
optionally, only retrieve transcript annotation data for the specified set of transcript ids. Default is NULL. |
splice_matrix |
whether generate a known exon splice matrix from the annotation. this is not necessary if you don't want to analyse junction results, default is FALSE. |
ClinVar |
whether to download ClinVar data, default is FALSE. |
... |
additional arguments |
several .RData file containing annotations needed for further analysis.
Xiaojing Wang
## Not run: transcript_ids <- c("NM_001126112", "NM_033360", "NR_073499", "NM_004448", "NM_000179", "NR_029605", "NM_004333", "NM_001127511") pepfasta <- system.file("extdata", "refseq_pro_seq.fasta", package="customProDB") CDSfasta <- system.file("extdata", "refseq_coding_seq.fasta", package="customProDB") annotation_path <- tempdir() PrepareAnnotationRefseq(genome='hg38', CDSfasta, pepfasta, annotation_path, dbsnp=NULL, transcript_ids=transcript_ids, splice_matrix=FALSE, ClinVar=FALSE) ## End(Not run)