search for: hg19

Need way to resize an existing graphics window. This should be applicable across platforms (as part of a package). Context: function1() draws main plot (I'm using grid), function2() adds smaller plot above main plot, but this one can sometimes overflow the original graphics window area. Thanks, Sigal

...ot;loop" to make the process automatic and fast? When compute each sample, the script type in R almost the same, just the input and output file's name is changed(chr1 change to chr2, chr3,chr4...). The first sample's script like this: >chr1=MEDIPS.readAlignedSeqences(BSgenome="hg19", file="chr1",numrows= ) >chr1=MEDIPS.genomeVector(data=chr1, bin_size=50,extend=250) ... ... >write.table(frameschr1.frame500.step250, file="frames.chr1.meth.txt", sep="\T", quote=F, col.names=T, row.names=F) The second sample's script like this: >c...

Hi I have an organism directory that contains two folders galGal3 and hg19 and many other files. orgDir = '/home/mary/org' When I try to use list.dir() function, it gives me the same answer, no matter what is the value of full.names argument. > list.dirs(path = indexDir, full.names = FALSE)[1] "/home/mary/org" [2] "/home/mary/org/galGal3&quo...

Hi, I was wondering I'm going about this in the correct way. I need to test if there are coding sequences or exons in hg19 which match a string of 100bp "D" i.e. [A,G or T]. However I'm getting a strange result. I get a hit on chr7, using the 100bp search however when I search with 60bp sequence of "D" I don't get any hits. library("BSgenome") library("Biostrings") lib...

...packages() finally returned with the following warnings and errors: Warning messages: 1: packages ?hgu133aprobe?, ?hgu95av2.db?, ?BSgenome.Celegans.UCSC.ce2?, ?BSgenome.Mmusculus.UCSC.mm10?, ?BSgenome.Dmelanogaster.UCSC.dm3.masked?, ?BSgenome.Hsapiens.UCSC.hg18.masked?, ?BSgenome.Hsapiens.UCSC.hg19.masked?, ?BSgenome.Mmusculus.UCSC.mm9.masked?, ?BSgenome.Scerevisiae.UCSC.sacCer2?, ?BSgenome.Hsapiens.NCBI.GRCh38?, ?BSgenome.Rnorvegicus.UCSC.rn5?, ?drosophila2probe?, ?hgu95av2probe?, ?hgu95av2cdf?, ?SNPlocs.Hsapiens.dbSNP.20100427?, ?SNPlocs.Hsapiens.dbSNP.20101109?, ?SNPlocs.Hsapiens.dbSN...

..._TELEPHONE=C LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] profvis_0.3.3 bindrcpp_0.2 [3] FDb.InfiniumMethylation.hg19_2.2.0 org.Hs.eg.db_3.4.1 [5] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.28.4 [7] AnnotationDbi_1.38.2 Biobase_2.36.2 [9] GenomicRanges_1.28.4 GenomeInfoDb_1.12.2 [11] IRanges_2.10.2 S4Vectors_0.14.3 [13] Bioc...