search for: hsapien

...packages() and after a long time the call to install.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?, ?SNPloc...

Hi all, I am using the package ChIPpeakAnno, and I have a problem with the function getAllPeakSequence. This is related to object oriented programming I think, I have the following message: > peaksWithSequences <- getAllPeakSequence(peakList, upstream = 100, > downstream = 100, genome = Hsapiens) Error in validObject(.Object) : invalid class "GRanges" object: superclass "Sequence" not defined in the environment of the object's class Is the error coming from my configuration or from the code? I do not know many things about OOP in R. Thanks. -- View this mess...

...g 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") library("BSgenome.Hsapiens.UCSC.hg19") library("biomaRt") library("GenomicFeatures") #extract the alignments which match real genes #(add this onto stefans script … req to buid the gr object using the regions from the BSgenome alignment of the 100bp seqs.) txdb <- makeTranscriptDbFromUCSC(ge...

...he above problem would be highly appreciated. > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] BSgenome.Hsapiens.UCSC.hg18_1.3.19 BSgenome_1.28.0 [3] methylPipe_0.99.0 Rsamtools_1.12.3 [5] Biostrings_2.28.0 GenomicRanges_1.12.4 [7] IRanges_1.18.1 GOstats_2.26.0 [9] RSQLite_0.11.4 DBI_0.2-7 [11] graph_1.38.2 Ca...

...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] BiocGenerics_0.22.0 epian_0.1.0...