Displaying 5 results from an estimated 5 matches for "hsapiens".
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sapiens
2015 Apr 18
2
truncated warning messages
...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?,
?SNPlocs...
2011 Sep 21
4
chippeakanno package: "getAllPeakSequence" problem
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 messa...
2011 Apr 15
1
Whole genome searching of 100bp "D" sequence
...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(gen...
2013 Jun 26
2
Error on executing functions from installed package
...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 Cat...
2017 Aug 24
3
Are r2dtable and C_r2dtable behaving correctly?
...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...