OutputVarprocodingseq {customProDB} | R Documentation |
Output 'snvprocoding'
OutputVarprocodingseq(vartable, procodingseq, ids, lablersid = FALSE, ...)
vartable |
A data frame which is the output of aaVariation(). |
procodingseq |
A dataframe containing protein ids and coding sequence for the protein. |
ids |
A dataframe containing gene/transcript/protein id mapping information. |
lablersid |
If includes the dbSNP rsid in the header of each sequence, default is FALSE. Must provide dbSNP information in function Positionincoding() if put TRUE here. |
... |
Additional arguments |
This function uses the output of aaVariation() as input, introduces the nonsynonymous variation into the protein database.
a data frame containing protein coding sequence proteins with single nucleotide 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']] == 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", "ids.RData", package="customProDB")) load(system.file("extdata/refseq", "proseq.RData", package="customProDB")) postable_snv <- Positionincoding(SNVvcf, exon, dbsnpinCoding) txlist <- unique(postable_snv[, 'txid']) codingseq <- procodingseq[procodingseq[, 'tx_id'] %in% txlist, ] mtab <- aaVariation (postable_snv, codingseq) OutputVarprocodingseq(mtab, codingseq, ids, lablersid=TRUE)