User: sun

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sun100
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Posts by sun

<prev • 12 results • page 1 of 2 • next >
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specify the color in plotMutationSpectrum() of SomaticSignatures library
... Hi All, How can I specify the color that I would like to use in plotMutationSpectrum()? eg. plotMutationSpectrum(sca_motifs, "study", normalize = TRUE), I would like to only use "red" color here,  or plotMutationSpectrum(sca_motifs, "study",colorby = c("alteration"), normalize = TRUE), if I woul ...
somaticsignatures written 3.8 years ago by sun100 • updated 3.8 years ago by Julian Gehring1.3k
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Any R Package To Detect Copy Neutral LOH for SNP 6.0 Array Data
... As I have known, PSCBS package can be used for CN-LOH detection. However, we would like to try more tools. I am wondering if there are any other tools or R packages available for CN-LOH detection. Thank you so much. Rebecca ...
snp microarray affy written 5.1 years ago by sun100
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autoplot() in ggbio package for txdb object
... Hello, I tried to draw the gene model by using autoplot() in ggbio package with the following codes. library(ggbio) library("TxDb.Hsapiens.UCSC.hg19.knownGene") txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene data(genesymbol, package = "biovizBase") autoplot(txdb,which = genesymbol["ACSS2"],names.e ...
ggbio written 5.4 years ago by sun100
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Can GAGE be used for transcript set pathway analysis
... Hello, I have the differential expressed transcript data, e,g TranscriptID Log2FC uc003jmh.1 -7.98049671088886 uc002alj.1 -9.19509271998651 I have converted transcriptIDs to keggEntrezs. uc003jmh.1 hsa04610+730 uc002alj.1 hsa04260+7168 Then I tried to use gage() to get the pat ...
pathways gage written 5.6 years ago by sun100 • updated 5.6 years ago by Luo Weijun1.5k
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Answer: A: transcriptDb object not found when call locateVariants() in a function
... > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.10.0 AnnotationDbi_1.20.0 Biobase_2.18.0 ...
written 6.9 years ago by sun100
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transcriptDb object not found when call locateVariants() in a function
... Hi I put locateVariants() in a test() function, save test() in "test.R" file. see bellow scripts, In "test.R" file, test <-function() { vcf <-readVcf("var.raw.vcf","Arabidopsis") rd <-rowData(vcf) txdb <-loadDb("Arabidopsis.sqlite") allvar <- locateVariants(rd,txdb, AllV ...
written 6.9 years ago by sun100
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DNAStringSet_translate error in predictCoding()
... Hi all, I got an error when I used predictCoding() in VariantAnnotation package. > coding <- predictCoding(vcf, txdb, injected_Arabi) Error in .Call2("DNAStringSet_translate", x, DNA_BASE_CODES, lkup, skipcode, : in 'x[[24606]]': not a base at pos 3 How can I get the value of x[[24606]]? ...
written 7.1 years ago by sun100 • updated 7.1 years ago by Valerie Obenchain6.7k
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Comment: C: predictCoding() return empty Granges
... Hi Valerie, After I loaded correct BSgenome: library(BSgenome.Athaliana.TAIR.TAIR9), the predictCoding() returned the coding SNPs results to me. However, the locateVariants() still had error message. rd <- rowData(vcf) intersect(seqlevels(vcf), seqlevels(txdb)) [1] "Chr1" > allvar <- l ...
written 7.2 years ago by sun100
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Comment: C: predictCoding() return empty Granges
... Hi Herve, Thanks for reminding me. I used library(BSgenome.Athaliana.TAIR.TAIR9) to instead. Rebecca On Fri, Oct 5, 2012 at 12:56 PM, Hervé Pagès wrote: > Hi Rebecca, > > > On 10/05/2012 11:31 AM, sun wrote: > >> Hi Valerie, >> >> I did make VCF object and Trans ...
written 7.2 years ago by sun100
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predictCoding() return empty Granges
... Hi Valerie, I did make VCF object and TranscriptDb with same chromosome name in my last test. I am still in trouble when I use locateVariants() and predictCoding() in newest released Bioconductor 2.11. I can use locateVariants() successfully in Bioconductor 2.10. Due to I can not adjust chr name of ...
annotation cancer arabidopsis thaliana bsgenome snplocs transcriptdb written 7.2 years ago by sun100 • updated 7.2 years ago by Hervé Pagès ♦♦ 14k

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Popular Question 3.8 years ago, created a question with more than 1,000 views. For predictCoding() return empty Granges

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