PrepareAnnotationGENCODE {proBAMr} | R Documentation |
prepare the annotation from GENCODE. Download GTF and FASTA files from GENCODE ftp first. Read introduction for more information.
PrepareAnnotationGENCODE(gtfFile, CDSfasta, pepfasta, annotation_path, dbsnp = NULL, splice_matrix = FALSE, COSMIC = FALSE, ...)
gtfFile |
specify GTF file location. |
CDSfasta |
path to the fasta file of coding sequence. |
pepfasta |
path to the fasta file of protein sequence. |
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. "snp135") |
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. |
COSMIC |
whether to download COSMIC data, default is FALSE. |
... |
additional arguments |
several .RData files containing annotations needed for further analysis.
Xiaojing Wang
gtfFile <- system.file("extdata", "test.gtf", package="proBAMr") CDSfasta <- system.file("extdata", "coding_seq.fasta", package="proBAMr") pepfasta <- system.file("extdata", "pro_seq.fasta", package="proBAMr") annotation_path <- tempdir() PrepareAnnotationGENCODE(gtfFile, CDSfasta, pepfasta, annotation_path, dbsnp=NULL, splice_matrix=FALSE, COSMIC=FALSE)