User: mms140130

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mms1401300
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Posts by mms140130

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how to find Snps that are within 1e6 from gene
... I have Snp data as follows (part of the data)     snp          chr         pos     rs987435    chr7    78599583     rs345783    chr15    33395779     rs955894    chr1    189807684     rs6088791    chr20    33907909     rs11180435    chr12    75664046     rs17571465    chr1    218890658     rs234272 ...
R written 10 months ago by mms1401300 • updated 10 months ago by Vincent J. Carey, Jr.6.2k
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how to analyze CNV data
... Hello, I'm trying to use copy number variation data in a statistical model "regression" so I have for example gene expression data and SNP data for breast cancer, which is one data point for each patient. the CNV data is different for each patient there are 23 chromosomes and several segment means ...
copy number written 10 months ago by mms1401300
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Comment: C: Mapping regions to gene symbols
...   @Vincent I had the following error too  subsetByOverlaps(genes(EnsDb.Hsapiens.v75), mygr) Error in genes(EnsDb.Hsapiens.v75) :    object 'EnsDb.Hsapiens.v75' not found in addition to I have tried the code and I used the r2syms as you wrote then > mygr = GRanges(ss$Chromosome, IRanges(ss$St ...
written 10 months ago by mms1401300
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Mapping regions to gene symbols
... I have used the code in another question https://support.bioconductor.org/p/67118/#97616,but it didn't work with me, I have those Segment_Mean, a start and end I want to know which genes overlap with those regions. xx = splitColumnByOverlap(gns, cnv, "SYMBOL") Warning message: In .Seqinfo.mergexy(x ...
annotation copynumber R written 10 months ago by mms1401300 • updated 10 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: Mapping genome regions to gene symbols
... @Martin Thanks for your answer, I got the following error  xx = splitColumnByOverlap(gns, cnv, "SYMBOL") Warning message: In .Seqinfo.mergexy(x, y) :   The 2 combined objects have no sequence levels in common. (Use   suppressWarnings() to suppress this warning.) my cnv is the copy number variation ...
written 10 months ago by mms1401300
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Comment: C: Mapping genome regions to gene symbols
... @Martin I'm trying to map CNV to genes, I had the following error when I applied your code symInCnv = splitByOverlap(gns, cnv, "SYMBOL") Error in findOverlaps(query, subject, ...) : object 'query' not found what should I do also I have 24 chromosomes , I would like to apply the code to the whole ...
written 10 months ago by mms1401300 • updated 10 months ago by Martin Morgan ♦♦ 21k

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