## ----echo=FALSE, results='hide', warning=FALSE, message=FALSE-------------- library(dagLogo) ## ----setenv, eval=FALSE, echo=TRUE----------------------------------------- # Sys.setenv(R_GSCMD=file.path("C:", "Program Files", "gs", # "gs9.06", "bin", "gswin32c.exe")) ## ----fetchSequences-------------------------------------------------------- library(dagLogo) library(biomaRt) try({##just in case biomaRt server does not response mart <- useMart("ensembl", "dmelanogaster_gene_ensembl") dat <- read.csv(system.file("extdata", "dagLogoTestData.csv", package="dagLogo")) dat <- dat[1:5,] ##subset to speed sample dat seq <- fetchSequence(as.character(dat$entrez_geneid), anchorPos=as.character(dat$NCBI_site), mart=mart, upstreamOffset=7, downstreamOffset=7) head(seq@peptides) }) ## ----fetchSequences2------------------------------------------------------- try({ seq <- fetchSequence(as.character(dat$entrez_geneid), anchorAA="*", anchorPos=as.character(dat$peptide), mart=mart, upstreamOffset=7, downstreamOffset=7) head(seq@peptides) }) ## ----fetchSequences3------------------------------------------------------- if(interactive()){ dat <- read.csv(system.file("extdata", "peptides4dagLogo.csv", package="dagLogo")) tail(dat) mart <- useMart("ensembl", "hsapiens_gene_ensembl") seq <- fetchSequence(toupper(as.character(dat$symbol)), type="hgnc_symbol", anchorAA="s", anchorPos=as.character(dat$peptides), mart=mart, upstreamOffset=7, downstreamOffset=7) head(seq@peptides) } ## ----formatSequence-------------------------------------------------------- dat <- unlist(read.delim(system.file("extdata", "grB.txt", package="dagLogo"), header=F, as.is=TRUE)) head(dat) ##prepare proteome from a fasta file proteome <- prepareProteome(fasta=system.file("extdata", "HUMAN.fasta", package="dagLogo")) ##prepare object of dagPeptides seq <- formatSequence(seq=dat, proteome=proteome, upstreamOffset=14, downstreamOffset=15) ## ----prepareProteome0------------------------------------------------------ if(interactive()){ library(UniProt.ws) UniProt.ws <- UniProt.ws(taxId=9606) proteome <- prepareProteome(UniProt.ws=UniProt.ws) } ## ----prepareProteome------------------------------------------------------- bg <- buildBackgroundModel(seq, bg="wholeGenome", proteome=proteome) ## ----testDAU--------------------------------------------------------------- t0 <- testDAU(seq, bg) t1 <- testDAU(seq, bg, group="classic") t2 <- testDAU(seq, bg, group="charge") t3 <- testDAU(seq, bg, group="chemistry") t4 <- testDAU(seq, bg, group="hydrophobicity") ## ----dagHeatmap,fig.cap="DAG heatmap",fig.width=6,fig.height=6------------- dagHeatmap(t0) ##Plot a heatmap to show the results ## ----dagLogo0,fig.cap="ungrouped results",fig.width=6,fig.height=4--------- dagLogo(t0) ##Plot a logo to show the ungrouped results ## ----dagLogo1,fig.cap="classic grouped",fig.width=6,fig.height=4----------- ##Plot a logo to show the classic grouped results dagLogo(t1, namehash=nameHash(t1@group), legend=TRUE) ## ----dagLogo2,fig.cap="charge grouped",fig.width=6,fig.height=4------------ ##Plot a logo to show the charge grouped results dagLogo(t2, namehash=nameHash(t2@group), legend=TRUE) ## ----dagLogo3,fig.cap="chemistry grouped",fig.width=6,fig.height=4--------- ##Plot a logo to show the chemistry grouped results dagLogo(t3, namehash=nameHash(t3@group), legend=TRUE) ## ----dagLogo4,fig.cap="hydrophobicity grouped",fig.width=6,fig.height=4---- ##Plot a logo to show the hydrophobicity grouped results dagLogo(t4, namehash=nameHash(t4@group), legend=TRUE) ## ----CAPmotif,fig.cap="Catobolite Activator Protein Motif",fig.width=6,fig.height=4---- library(motifStack) protein<-read.table(file.path(find.package("motifStack"),"extdata","cap.txt")) protein<-t(protein[,1:20]) motif<-pcm2pfm(protein) motif<-new("pfm", mat=motif, name="CAP", color=colorset(alphabet="AA",colorScheme="chemistry")) ##The DNA-binding helix-turn-helix motif of the CAP family ploted by motifStack plot(motif) ## ----CAPdagLogo,fig.cap="Catobolite Activator Protein Motif",fig.width=6,fig.height=4---- library(Biostrings) cap <- as.character(readAAStringSet(system.file("extdata", "cap.fasta", package="dagLogo"))) data(ecoli.proteome) seq <- formatSequence(seq=cap, proteome=ecoli.proteome) bg <- buildBackgroundModel(seq, bg="wholeGenome", proteome=ecoli.proteome, permutationSize=10L) ##The DNA-binding helix-turn-helix motif of the CAP family ploted by dagLogo t0 <- testDAU(seq, bg) dagLogo(t0) ## ----CAPgroup,fig.cap="Catobolite Activator Protein Motif",fig.width=6,fig.height=4---- ## The DNA-binding helix-turn-helix motif of the CAP family grouped by chemistry t1 <- testDAU(seq, bg, group="chemistry") dagLogo(t1, namehash=nameHash(t1@group), legend=TRUE) ## ----sessionInfo----------------------------------------------------------- sessionInfo()