Positionincoding {customProDB} | R Documentation |
For those variations labeled with "Coding", positionincoding() function computes the position of variation in the coding sequence of each transcript.
Positionincoding(Vars, exon, dbsnp = NULL, COSMIC = NULL, ...)
Vars |
a GRanges object of variations |
exon |
a dataframe of exon annotations for protein coding transcripts. |
dbsnp |
provide a GRanges object of known dbsnp information to include dbsnp evidence into the output table, default is NULL. |
COSMIC |
provide a GRanges object of known COSMIC information to include COSMIC evidence into the output table, default is NULL. |
... |
additional arguments |
this function prepares input data frame for aaVariation().
a data frame containing the position in coding sequence for each variation
Xiaojing Wang
vcffile <- system.file("extdata/vcfs", "test1.vcf", package="customProDB") vcf <- InputVcf(vcffile) table(values(vcf[[1]])[['INDEL']]) index <- which(values(vcf[[1]])[['INDEL']] == TRUE) indelvcf <- vcf[[1]][index] index <- which(values(vcf[[1]])[['INDEL']] == FALSE) SNVvcf <- vcf[[1]][index] load(system.file("extdata/refseq", "exon_anno.RData", package="customProDB")) load(system.file("extdata/refseq", "dbsnpinCoding.RData", package="customProDB")) load(system.file("extdata/refseq", "procodingseq.RData", package="customProDB")) load(system.file("extdata/refseq", "cosmic.RData", package="customProDB")) postable_snv <- Positionincoding(SNVvcf, exon, dbsnpinCoding, COSMIC=cosmic)