1. MotifDb
  2. Commit 4de1d63a6cc240b488182bd51cb2bd81fa18604d
Browse code

merge

paul-shannon authored on 23/03/2022 21:48:50
Showing 24 changed files
.Rbuildignore
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@@ -1,2 +1,7 @@
1 1 
 ^doc$
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 ^Meta$
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+inst/scripts
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+misc/
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+notInstalled/
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+explore/
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+inst/unitTests/*.RData
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\ No newline at end of file
DESCRIPTION
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@@ -1,8 +1,8 @@
1 1 
 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.35.5
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-Date: 2021-09-01
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+Version: 1.37.2
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+Date: 2022-03-04
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 Author: Paul Shannon, Matt Richards
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 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
R/MotifList-class.R
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@@ -247,7 +247,7 @@ setMethod('show', 'MotifList',
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       if (length (object) == 0)
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         return ()
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-      cat ('| Created from downloaded public sources: 2013-Aug-30', '\n', sep='')
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+      cat ('| Created from downloaded public sources, last update: 2022-Mar-04', '\n', sep='')
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       tbl.dataSource = as.data.frame (table (mcols (object)$dataSource))
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       tbl.org = as.data.frame (table (mcols (object)$organism))
R/zzz.R
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@@ -13,6 +13,7 @@ MotifDb <- NULL
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     for(data.file in data.files) {
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        # define these to keep 'check' happy.  they are loaded by 'load'
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       tbl.md = NA; matrices = NA;
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+      # print(noquote(sprintf("--- about to load and append from file '%s'", data.file)))
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       variables = load(data.file)
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       mdb = append(mdb, MotifList(matrices, tbl.md))
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       if(!quiet)
explore/motifMatchingDistributions/chip-matching.R
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+library(MotifDb)
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+library(trena)   # only for MotifMatcher
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+library(igvR)
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+library(chipDB)
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+
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+#------------------------------------------------------------------------------------------------------------------------
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+targetGene <- "GATA2"
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+tf <- "ZNF263"
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+motif <- query(MotifDb, c("sapiens", tf, "jaspar2018"))
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+stopifnot(length(motif) == 1)
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+
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+igv <- igvR()
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+setGenome(igv, "hg38")
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+showGenomicRegion(igv, "GATA2")
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+getGenomicRegion(igv)
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+
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+tbl.region <- with(getGenomicRegion(igv), data.frame(chrom=chrom, start=start, end=end, stringsAsFactors=FALSE))
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+
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+matcher <- MultiMethodMotifMatcher("hg38", as.list(motif), tbl.region, "Biostrings matchPWM", .80)
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+
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+
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+tbl.enhancers <- get(load(system.file(package="TrenaProject", "extdata", "genomeAnnotation", "geneHancer.v4.7.allGenes.RData")))
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+tbl.targetGeneEnhancers <- subset(tbl.enhancers, geneSymbol==targetGene)
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+track <- DataFrameQuantitativeTrack("enhancers", tbl.targetGeneEnhancers[, c("chrom", "start", "end", "combinedScore")],
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+                                    autoscale=FALSE, min=0, max=50, color="brown")
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+displayTrack(igv, track)
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+showGenomicRegion(igv, "chr3:128,470,539-128,502,070")
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+
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+
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+motifMatcher <- MotifMatcher("hg38", as.list(motif))
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+tbl.out <- findMatchesByChromosomalRegion(motifMatcher, tbl.region, pwmMatchMinimumAsPercentage=80)[, c(2,3,4,7)]
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+
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+track <- DataFrameQuantitativeTrack("moods-ZNF263", tbl.out, autoscale=TRUE, color="blue")
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+displayTrack(igv, track)
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+
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+cdb <- chipDB(quiet=FALSE)
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+tbl.cdb <- with(getGenomicRegion(igv), getHits(cdb, chrom, start, end))
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+tbl.csHits <- subset(tbl.cdb, tf=="ZNF263")
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+track <- DataFrameAnnotationTrack(sprintf("%s-chip", tf), tbl.csHits[,c(1,2,3,5)], color="red")
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+displayTrack(igv, track)
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+
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+
explore/motifMatchingDistributions/mmd.R
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+library(MotifDb)
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+library(TrenaViz)   # only for MultiMethodMotifMatcher
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+library(igvR)
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+igv <- igvR()
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+igvR::setGenome(igv, "hg38")
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+showGenomicRegion(igv, "GATA2")
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+
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+library(TrenaProjectErythropoiesis)
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+tp <- TrenaProjectErythropoiesis()
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+setTargetGene(tp, "GATA2")
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+
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+tbl.enhancers <- getEnhancers(tp)[, c(1,2,3,5)]
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+
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+track <- DataFrameQuantitativeTrack("GH", tbl.enhancers,
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+                                    autoscale=FALSE, min=0, max=50, color="brown")
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+displayTrack(igv, track)
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+tbl.bigRegion <- with(tbl.enhancers, data.frame(chrom=tbl.enhancers$chrom[1], start=min(start)-5000, end=max(end)+5000),
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+                      stringsAsFactors=FALSE)
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+
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+bigRegion <- with(tbl.enhancers, sprintf("%s:%d-%d", chrom=tbl.enhancers$chrom[1], start=min(start)-5000, end=max(end)+5000))
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+showGenomicRegion(igv, bigRegion)
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+
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+motif.tbx15 <- query(MotifDb, c("TBX15", "sapiens"), "jaspar2018")
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+m4.biostrings <- MultiMethodMotifMatcher("hg38", as.list(motif.tbx15), tbl.bigRegion, "Biostrings matchPWM", .80)
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+tbl.tbx15 <- matchMotifInSequence(m4.biostrings)
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+dim(tbl.tbx15)
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+track <- DataFrameQuantitativeTrack("matchPWM-tbx15", tbl.tbx15[, c(1,2,3,6)], autoscale=TRUE, color="blue")
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+displayTrack(igv, track)
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+
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+
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+motif.znf263 <- query(MotifDb, c("sapiens", "ZNF263", "jaspar2018"))
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+
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+tbl.znf263 <- matchMotifInSequence(m4.biostrings)
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+dim(tbl.znf263)
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+tbl.znf263$chrom <- as.character(tbl.znf263$chrom)
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+
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+
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+tbl.tbx15$chrom <- as.character(tbl.tbx15$chrom)
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+track <- DataFrameQuantitativeTrack("jaspar2018-TBX15-MA0803.1", tbl.tbx15[, c(1,2,3,6)], autoscale=TRUE, color="blue")
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+displayTrack(igv, track)
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+
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+m4.moods <- MultiMethodMotifMatcher("hg38", as.list(motif), tbl.bigRegion, "MOODS matchMotifs", 6)
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+tbl.tbx15.2 <-  matchMotifInSequence(m4.moods)
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+dim(tbl.tbx15.2)
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+track <- DataFrameQuantitativeTrack("moods jaspar2018-TBX15-MA0803.1", tbl.tbx15.2[, c(1,2,3,6)], autoscale=TRUE, color="green")
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+displayTrack(igv, track)
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+
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+
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+library(FimoClient)
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+
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+FIMO_HOST <- "localhost"
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+FIMO_PORT <- 600161
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+if(!exists("fimoServerStarted")){
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+   fimoServerStarted <- TRUE
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+   export(motif, con="motif.meme", format="meme")
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+   cmd <- sprintf("make -f ~/github/fimoService/server/makefile", PORT=%d MOTIFS=motif.meme", FIMO_PORT)
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+   system(cmd)
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+   #meme.file <- system.file(package="FimoClient", "extdata", "human.jaspar2018.meme")
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+   #stopifnot(file.exists(meme.file))
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+   #cmd <- sprintf("make -f ~/github/fimoService/server/makefile PORT=%d MOTIFS=%s", FIMO_PORT, meme.file)
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+   #print(cmd)
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+   #system(cmd)
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+   printf("--- sleeping 5, making sure fimo server is awake")
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+   Sys.sleep(5)
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+   }
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+
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+
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+fc <- FimoClient(FIMO_HOST, FIMO_PORT, quiet=FALSE)
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+tbl.fimo <- requestMatchForRegions(fc, tbl.bigRegion, "hg38", pvalThreshold=0.00006)
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+track <- DataFrameQuantitativeTrack("fimo jaspar2018-TBX15-MA0803.1", tbl.fimo[, c(1,2,3,6)], autoscale=TRUE, color="darkred")
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+displayTrack(igv, track)
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+
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+tbl.fimo.qScore <- tbl.fimo[, c(1,2,3,8)]
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+tbl.fimo.qScore$qValue <- -log10(tbl.fimo.qScore$qValue)
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+track <- DataFrameQuantitativeTrack("fimo qScore TBX15", tbl.fimo.qScore[, c(1,2,3,4)], autoscale=TRUE, color="orange")
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+displayTrack(igv, track)
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+
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+
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+library(chipDB)
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+cdb <- chipDB(quiet=FALSE)
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+tbl.cdb <- with(getGenomicRegion(igv), getHits(cdb, chrom, start, end))
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+
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+tbl.tf <- as.data.frame(table(tbl.cdb$tf))
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+colnames(tbl.tf) <- c("tf", "count")
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+tbl.tf <- tbl.tf[order(tbl.tf$count, decreasing=TRUE),]
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+tfs <- unique(tbl.cdb$tf)
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+length(tfs)
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+
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+
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+genesInModelForMarjorie <- c("FOXM1", "RELA", "GATA1", "PAX6", "ATF2", "GTF2I", "ELK3", "SREBF2", "TBX15", "VDR", "PATZ1",
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+                             "SIN3A", "RFX5", "ZNF263", "BATF", "PLAGL1", "MYB")
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+length(genesInModelForMarjorie)  # [1] 17
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+subset(tbl.tf, tf %in% genesInModelForMarjorie)   # 10
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+ #         tf count
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+ # 218  SIN3A    44
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+ # 206   RELA    21
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+ # 90   GATA1    11
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+ # 291 ZNF263    10
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+ # 273    VDR     8
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+ # 85   FOXM1     5
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+ # 154    MYB     5
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+ # 208   RFX5     4
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+ # 239 SREBF2     2
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+ # 12    ATF2     1
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+
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+track <- DataFrameAnnotationTrack("ZNF263", subset(tbl.cdb, tf=="ZNF263")[, c("chrom", "start", "end", "tissueOrCellType")])
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+displayTrack(igv, track)
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+
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+motif.znf263 <- query(MotifDb, c("sapiens", "ZNF263", "jaspar2018"))
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+
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+tbl.region <- with(getGenomicRegion(igv), data.frame(chrom=chrom, start=start, end=end, stringsAsFactors=FALSE))
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+m4.biostrings <- MultiMethodMotifMatcher("hg38", as.list(motif.znf263), tbl.region, "Biostrings matchPWM", .75)
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+tbl.znf263 <- matchMotifInSequence(m4.biostrings)
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+dim(tbl.znf263)
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+tbl.znf263$chrom <- as.character(tbl.znf263$chrom)
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+track <- DataFrameQuantitativeTrack("moods-ZNF263", tbl.znf263[, c(1,2,3,6)], autoscale=TRUE, color="blue")
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+displayTrack(igv, track)
explore/motifMatchingDistributions/motif.meme
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+MEME version 4
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+
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+ALPHABET= ACGT
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+
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+strands: + -
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+
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+Background letter frequencies
8 
+A 0.250 C 0.250 G 0.250 T 0.250
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+
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+MOTIF Hsapiens-jaspar2018-TBX15-MA0803.1
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+letter-probability matrix: alength= 4 w= 8 nsites= 45 E=8.1e-020
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+ 0.9251233263  0.0065186751  0.0584918957  0.0098661029
13 
+ 0.0410247223  0.0090469366  0.9407022573  0.0092260838
14 
+ 0.0018047112  0.0006648936  0.9975303951  0.0000000000
15 
+ 0.0055540381  0.0159337157  0.0223072020  0.9562050442
16 
+ 0.0000000000  0.0007611798  0.9992388202  0.0000000000
17 
+ 0.0122796246  0.0381545478  0.0284185598  0.9211472678
18 
+ 0.0036860183  0.0380330066  0.8797855408  0.0784954344
19 
+ 0.9569020501  0.0064692483  0.0278815490  0.0087471526
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+
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+
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+
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+
explore/newFlyFactor/UmassPGFE_PWMfreq_PublicDatasetA_20220210.txt
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