fetch sequence by id

Description

fetch amino acid sequence by given identifiers via biomaRt or proteome prepared by prepareProteome

Usage

fetchSequence(IDs, type="entrezgene", anchorAA=NULL, anchorPos,
                            mart, proteome, upstreamOffset, downstreamOffset)

Arguments

Value

return an object of dagPeptides

Author(s)

Jianhong Ou, Alexey Stukalov, Julie Zhu

See Also

formatSequence

Examples

if(interactive()){
    mart <- useMart("ensembl", "dmelanogaster_gene_ensembl")
    dat <- read.csv(system.file("extdata", "dagLogoTestData.csv", package="dagLogo"))
    seq <- fetchSequence(as.character(dat$entrez_geneid[1:5]), 
                anchorPos=as.character(dat$NCBI_site[1:5]), 
                mart=mart, 
                upstreamOffset=7, 
                downstreamOffset=7)
    ## sample: use sequence as anchorPos
    sequences <- seq@peptides
    sequences[, 8] <- "k"
    sequences <- apply(sequences, 1, paste, collapse="")
    seq <- fetchSequence(as.character(seq@data$IDs),
                        anchorAA="k",
                        anchorPos=sequences,
                        mart=mart,
                        upstreamOffset=7,
                        downstreamOffset=7)
    ## sample: use sequence as anchorPos 2
    sequences <- cbind(seq@peptides[, 1:8], "*", seq@peptides[, 9:15])
    sequences <- apply(sequences, 1, paste, collapse="")
    seq <- fetchSequence(as.character(seq@data$IDs),
                        anchorAA="*",
                        anchorPos=sequences,
                        mart=mart,
                        upstreamOffset=7,
                        downstreamOffset=7)
}

Results

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)

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Type 'license()' or 'licence()' for distribution details.

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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(dagLogo)
Loading required package: biomaRt
Loading required package: grImport
Loading required package: grid
Loading required package: XML
Loading required package: motifStack
Loading required package: MotIV
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


Attaching package: 'MotIV'

The following object is masked from 'package:stats':

    filter

Loading required package: ade4

Attaching package: 'ade4'

The following object is masked from 'package:BiocGenerics':

    score

Loading required package: Biostrings
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: IRanges
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dagLogo/fetchSequence.Rd_%03d_medium.png", width=480, height=480)
> ### Name: fetchSequence
> ### Title: fetch sequence by id
> ### Aliases: fetchSequence
> ### Keywords: misc
> 
> ### ** Examples
> 
> #if(interactive()){
>     mart <- useMart("ensembl", "dmelanogaster_gene_ensembl")
>     dat <- read.csv(system.file("extdata", "dagLogoTestData.csv", package="dagLogo"))
>     seq <- fetchSequence(as.character(dat$entrez_geneid[1:5]), 
+                 anchorPos=as.character(dat$NCBI_site[1:5]), 
+                 mart=mart, 
+                 upstreamOffset=7, 
+                 downstreamOffset=7)
>     ## sample: use sequence as anchorPos
>     sequences <- seq@peptides
>     sequences[, 8] <- "k"
>     sequences <- apply(sequences, 1, paste, collapse="")
>     seq <- fetchSequence(as.character(seq@data$IDs),
+                         anchorAA="k",
+                         anchorPos=sequences,
+                         mart=mart,
+                         upstreamOffset=7,
+                         downstreamOffset=7)
>     ## sample: use sequence as anchorPos 2
>     sequences <- cbind(seq@peptides[, 1:8], "*", seq@peptides[, 9:15])
>     sequences <- apply(sequences, 1, paste, collapse="")
>     seq <- fetchSequence(as.character(seq@data$IDs),
+                         anchorAA="*",
+                         anchorPos=sequences,
+                         mart=mart,
+                         upstreamOffset=7,
+                         downstreamOffset=7)
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>