## ---- echo=FALSE, results="hide", warning=FALSE---------------------------- suppressPackageStartupMessages({ library('generegulation') }) ## ----echo=FALSE------------------------------------------------------------ ## grImport is temporarily not available for Mac as a binary if (Sys.info()['sysname'] == "Darwin" && (!"grImport" %in% rownames(installed.packages()))) { library(BiocInstaller) biocLite("grImport", type="source") } ## ----echo=FALSE------------------------------------------------------------ ## move along, nothing to see here if (Sys.getenv("NODE_NAME") == "master") { seqLogo <- function(x) { fs=10 seqLogo::seqLogo(x, xfontsize=fs, yfontsize=fs) } } ## ----eval=FALSE------------------------------------------------------------ # ## try http:// if https:// URLs are not supported # source("https://bioconductor.org/biocLite.R") # biocLite(c("MotifDb", "GenomicFeatures", # "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene", # "org.Sc.sgd.db", "BSgenome.Scerevisiae.UCSC.sacCer3", # "motifStack", "seqLogo")) ## ----echo=FALSE------------------------------------------------------------ suppressPackageStartupMessages(library(MotifDb)) suppressPackageStartupMessages(library(S4Vectors)) suppressPackageStartupMessages(library(seqLogo)) suppressPackageStartupMessages(library(motifStack)) suppressPackageStartupMessages(library(Biostrings)) suppressPackageStartupMessages(library(GenomicFeatures)) suppressPackageStartupMessages(library(org.Sc.sgd.db)) suppressPackageStartupMessages(library(BSgenome.Scerevisiae.UCSC.sacCer3)) suppressPackageStartupMessages(library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)) ## -------------------------------------------------------------------------- library(MotifDb) library(S4Vectors) library(seqLogo) library(motifStack) library(Biostrings) library(GenomicFeatures) library(org.Sc.sgd.db) library(BSgenome.Scerevisiae.UCSC.sacCer3) library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene) ## -------------------------------------------------------------------------- library(MotifDb) library(seqLogo) library(motifStack) library(Biostrings) library(GenomicFeatures) library(org.Sc.sgd.db) library(BSgenome.Scerevisiae.UCSC.sacCer3) library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene) query(MotifDb, "DAL80") pfm.dal80.jaspar <- query(MotifDb,"DAL80")[[1]] seqLogo(pfm.dal80.jaspar) dal1 <- "YIR027C" chromosomal.loc <- transcriptsBy(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, by="gene") [dal1] promoter.dal1 <- getPromoterSeq(chromosomal.loc, Scerevisiae, upstream=1000, downstream=0) pcm.dal80.jaspar <- round(100 * pfm.dal80.jaspar) matchPWM(pcm.dal80.jaspar, unlist(promoter.dal1)[[1]], "90%") ## -------------------------------------------------------------------------- query(MotifDb,"DAL80") ## -------------------------------------------------------------------------- dal80.jaspar <- query(MotifDb,"DAL80")[[1]] dal80.scertf <-query(MotifDb,"DAL80")[[2]] seqLogo(dal80.jaspar) seqLogo(dal80.scertf) ## ---- dev="jpeg"----------------------------------------------------------- pfm.dal80.jaspar <- new("pfm", mat=query(MotifDb, "dal80")[[1]], name="DAL80-JASPAR") pfm.dal80.scertf <- new("pfm", mat=query(MotifDb, "dal80")[[2]], name="DAL80-ScerTF") plotMotifLogoStack(DNAmotifAlignment(c(pfm.dal80.scertf, pfm.dal80.jaspar))) ## -------------------------------------------------------------------------- query(MotifDb, "gat1") ## ---- dev="jpeg"----------------------------------------------------------- pfm.gat1.jaspar = new("pfm", mat=query(MotifDb, "gat1")[[1]], name="GAT1-JASPAR") pfm.gat1.scertf = new("pfm", mat=query(MotifDb, "gat1")[[2]], name="GAT1-ScerTF") pfm.gat1.uniprobe = new("pfm", mat=query(MotifDb, "gat1")[[3]], name="GAT1-UniPROBE") plotMotifLogoStack(c(pfm.gat1.uniprobe, pfm.gat1.scertf, pfm.gat1.jaspar)) ## -------------------------------------------------------------------------- pfm.dal80.scertf <- query(MotifDb, "dal80")[[2]] pcm.dal80.scertf <- round(100 * pfm.dal80.scertf) pfm.gat1.jaspar <- query(MotifDb, "gat1")[[1]] pcm.gat1.jaspar <- round(100 * pfm.gat1.jaspar) pfm.gat1.scertf <- query(MotifDb, "gat1")[[2]] pcm.gat1.scertf <- round(100 * pfm.gat1.scertf) ## -------------------------------------------------------------------------- genes <- c("DAL1", "DAL2", "DAL4", "DAL5", "DAL7", "DAL80", "GAP1") orfs <- as.character(mget(genes, org.Sc.sgdCOMMON2ORF)) ## -------------------------------------------------------------------------- grl <- transcriptsBy(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, by="gene") [orfs] ## -------------------------------------------------------------------------- promoter.seqs <- getPromoterSeq(grl, Scerevisiae, upstream=1000, downstream=0) ## -------------------------------------------------------------------------- pfm.dal80.scertf ## -------------------------------------------------------------------------- print (class(promoter.seqs)) promoter.seqs <- unlist(promoter.seqs) print (class(promoter.seqs)) matchPWM(pcm.dal80.scertf, promoter.seqs[[1]], "90%") ## -------------------------------------------------------------------------- pwm.hits <- sapply(promoter.seqs, function(pseq) matchPWM(pcm.dal80.scertf, pseq, min.score="90%")) ## -------------------------------------------------------------------------- dal80.scertf.hits <- sapply(promoter.seqs, function(pseq) matchPWM(pcm.dal80.scertf, pseq, min.score="90%")) gat1.scertf.hits <- sapply(promoter.seqs, function(pseq) matchPWM(pcm.gat1.scertf, pseq, min.score="90%")) gat1.jaspar.hits <- sapply(promoter.seqs, function(pseq) matchPWM(pcm.gat1.jaspar, pseq, min.score="90%")) ## -------------------------------------------------------------------------- dal80.scertf <- sapply(dal80.scertf.hits, length) gat1.jaspar <- sapply(gat1.jaspar.hits, length) gat1.scertf <- sapply(gat1.scertf.hits, length) ## -------------------------------------------------------------------------- tbl.gata <- data.frame(gene=genes, dal80.scertf, gat1.jaspar, gat1.scertf) ## ----eval=FALSE------------------------------------------------------------ # browseVignettes(package="MotifDb") ## ----eval=FALSE------------------------------------------------------------ # help.start() ## -------------------------------------------------------------------------- sessionInfo()