A data frame which is the output of
aaVariation().
proteinseq
A dataframe containing protein ids and
the protein sequence.
outfile
Output file name.
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.
RPKM
If includes the RPKM value in the header of
each sequence, default is NULL.
...
Additional arguments
Details
This function uses the output of aaVariation() as input,
introduces the nonsynonymous variation into the protein
database.
Value
FASTA file containing proteins with single nucleotide
variation.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(customProDB)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: biomaRt
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/customProDB/OutputVarproseq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: OutputVarproseq
> ### Title: Output the variant(SNVs) protein sequences into FASTA format
> ### Aliases: OutputVarproseq
>
> ### ** Examples
>
> vcffile <- system.file("extdata/vcfs", "test1.vcf", package="customProDB")
> vcf <- InputVcf(vcffile)
> table(values(vcf[[1]])[['INDEL']])
FALSE TRUE
54 7
> 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)
> outfile <- paste(tempdir(), '/test_snv.fasta',sep='')
> OutputVarproseq(mtab, proteinseq, outfile, ids, lablersid=TRUE)
>
>
>
>
>
> dev.off()
null device
1
>