User: Lna

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Lna0
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Posts by Lna

<prev • 30 results • page 3 of 3 • next >
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Comment: C: Distance calculation for variants in intergenic regions
... Everything should be uptodate now. I deleted R and all Bioconductor packages but the problem remains. > sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.1 LTS locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C LC_TIME ...
written 3.0 years ago by Lna0
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Comment: C: Distance calculation for variants in intergenic regions
... I removed R and Bioconductor completely and installed the new versions. I was also thinking that there should be no loop, but somehow it doesn't work for me. p_ids <- unlist(loc_int$FOLLOWID, use.names=FALSE) exp_ranges <- rep(loc_int,  elementNROWS(loc_int$FOLLOWID)) p_dist <- distance( ...
written 3.0 years ago by Lna0
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Upgrade to Bioconductor 3.4 - problems with R
... Hi, I was trying to upgrade to Bioconductor 3.4 and in order to do so I had to make an R upgrade (3.2.2 to 3.3.2). When running biocLite("BiocUpgrade") I get the error: Bioconductor version 3.4 cannot be upgraded with R version 3.3.2 I already tried to remove BiocInstaller with remove.packages ...
bioclite r update upgrade written 3.1 years ago by Lna0 • updated 3.1 years ago by James W. MacDonald52k
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Comment: C: Distance calculation for variants in intergenic regions
... Ok, thank you, I'll try that. So you get the same list of distances (printed above), but "normal" distances except of the NA entries? ...
written 3.1 years ago by Lna0
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Comment: C: Distance calculation for variants in intergenic regions
... GRanges object with 1 range and 5 metadata columns: seqnames ranges strand | paramRangeID REF ALT QUAL FILTER <Rle> <IRanges> <Rle> | <factor> <DNAStringSet> <DNAStringSetList> <numer ...
written 3.1 years ago by Lna0
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Comment: C: Distance calculation for variants in intergenic regions
... You are right that I have to take care of the out of bounds case for results with fewer than three elements, but the NA entries are surely not coming from that, since my print statement comes before cutting the list to three elements. I am printing the complete list here, input list as well as outpu ...
written 3.1 years ago by Lna0
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Comment: C: Distance calculation for variants in intergenic regions
... locateVariants can find the closest one? As far as I understood it, it just provides a seemingly unsorted list of all genes within the user defined region (?). Which is not much of a problem if I can obtain the respective distances with the "distance()" function and order by distance. The problem is ...
written 3.1 years ago by Lna0
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Distance calculation for variants in intergenic regions
... Hi, I want to determine the three genes which are closest to my annotated intergenic variants in both directions. After annotating the variant list, I used commands which are part of the examples of locateVariants in the variantannotation package. This is what I tried: loc <- locateVariants(t ...
variantannotation genomicfeatures locatevariants written 3.1 years ago by Lna0 • updated 3.1 years ago by Michael Lawrence11k
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Use of org.Hs.eg.db and TxDb.Hsapiens.UCSC.hg19.knownGene
... Hi, I was trying to make a list of SNPs and names of genes they are related to. So I used the VariantAnnotation package  locateVariants(target, TxDb.Hsapiens.UCSC.hg19.knownGene, AllVariants()) and got a list of the respective geneids. As far as I understood VariantAnnotation gets the geneids fr ...
org.hs.eg.db txdb.hsapiens.ucsc.hg19.knowngene written 3.1 years ago by Lna0 • updated 3.1 years ago by Vincent J. Carey, Jr.6.3k
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GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
... Hi, I am completely new to sequence analysis and a want to perform a GWAS analysis using an Illumina HumanOmni5 BeadChip. I received data of my 16 samples, which incluce jpeg and idat files 3 tables in txt format (full data, snp and sample). I was looking for a recommended Workflow (any suggestio ...
qualitycontrol gwastools illumina humanomni5-4beadchip genomestudio written 3.6 years ago by Lna0 • updated 3.6 years ago by Stephanie M. Gogarten740

Latest awards to Lna

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Use of org.Hs.eg.db and TxDb.Hsapiens.UCSC.hg19.knownGene
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Upgrade to Bioconductor 3.4 - problems with R
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Upgrade to Bioconductor 3.4 - problems with R

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