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User: Christian Ruckert

Reputation:
170
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Trusted
Location:
Germany
Last seen:
2 years, 7 months ago
Joined:
10 years ago
Email:
c*******@uni-muenster.de

Posts by Christian Ruckert

<prev • 19 results • page 1 of 2 • next >
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Efficient coverage calculation with RleList and GRanges
... I am interested in calculating the average coverage and the percent of bases covered more than x-times for a large number of regions. My current and working approach is: 1. Calculate the coverage for every position in the genome (cov is a SimpleRleList): cov <- coverage(BamFile) 2. Subset to ...
coverage granges rle view mean written 2.6 years ago by Christian Ruckert170 • updated 2.6 years ago by Michael Lawrence10k
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biomaRt getBM returns allele as logical instead of character
... The following biomaRt query returns the minor_allele column as logical instead of character:   library("biomaRt") mart <- useMart(host="feb2014.archive.ensembl.org", biomart="ENSEMBL_MART_SNP") ensembl <- useDataset("hsapiens_snp", mart=mart) res <- getBM(attributes=c("chr_name","chrom ...
biomart error getbm logical written 3.1 years ago by Christian Ruckert170
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readVcf error resulting from star * in alt allele field
... I get the following error when trying to read in a VCF file: Error in .Call2("new_XStringSet_from_CHARACTER", ans_class, ans_elementType, : key 42 (char '*') not in lookup table   The problematic entry is: 3    37067095    .    ATATATTTTTT    *    11571.2    PASS    AC=1;AC_Orig=7;AF=0.5;AF ...
variantannotation written 3.4 years ago by Christian Ruckert170 • updated 3.4 years ago by Valerie Obenchain6.7k
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pintersect GRanges with empty results
... Hi all, I am searching a solution for the following problem: I have two GRanges objects, one with exon coordinates e.g. chr1 400 600 gene1 exon1 chr1 800 900 gene1 exon2 chr7 100 200 gene2 exon1 chr7 300 500 gene2 exon2 and one with the correspondi ...
written 4.5 years ago by Christian Ruckert170 • updated 4.5 years ago by Michael Lawrence60
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Answer: A: Regarding the commands for finding installed packages
... Use the library() command to list all installed packages. Kind regards, Christian Am 03.10.2012 08:09, schrieb manisha [guest]: > kindly tell me the command for listing all the packages i have installed on my system. > > > -- output of sessionInfo(): > > tried out the list() co ...
written 6.4 years ago by Christian Ruckert170
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Annotate Affy SNP6 probes in bioc
... I have a list of probesets from the Affymetrix GenomeWideSNP6 chip (e.g. CN_1111671, SNP_A-8305771) and want to annotate them in bioconductor, mainly with genome coordinates. Is there any easy to use annotation package like for the HGU133A chip? I know of NetAFFX, but I would like to circumvent the ...
hgu133a annotate written 6.4 years ago by Christian Ruckert170 • updated 6.4 years ago by Vincent J. Carey, Jr.6.3k
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Unambiguously mapping of affy IDs to gene symbols using hgu133plus2.db
... Hi, I am doing some mapping of affymetrix probeset IDs to gene symbols using package hgu133plus2.db. As the following example illustrates, each of the 40686 mapped probesets maps to exactly one gene symbol. > library("hgu133plus2.db") > x <- hgu133plus2SYMBOL > Llength(x) [1] 54675 ...
annotation hgu133plus2 biomart written 8.4 years ago by Christian Ruckert170 • updated 8.4 years ago by Marc Carlson7.2k
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Answer: A: How to normalize one additional CEL file?
... See bioconductor package RefPlus for an implementation of the RMA normalization which stores normalization parameters for later use on additional samples. Greetings, Christian Am 12.08.2010 15:20, schrieb Wiktor Mazin: > Dear List, > > Suppose you normalize a training set in some way (RM ...
written 8.5 years ago by Christian Ruckert170
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Limit for chromosomal regions in biomaRt?
... I have a character vector of approximately 25000 genomic regions I want to retrieve additional genomic information for using biomaRt R-package: library("biomaRt") mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl") regions = c( "1:661517:668171", "1:787463:794591" ...) attribs = c("chrom ...
biomart written 8.6 years ago by Christian Ruckert170 • updated 8.6 years ago by Steffen500
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AgiMicroRna readMicroRnaAFE error
... I have data from Agilent Human miRNA Microarray Version3 chips which were extracted using FeatureExtractor 10.5.1.1. When trying to invoke readMicroRnaAFE on these files I get the following error: dd.micro = readMicroRnaAFE(targets.micro, verbose=TRUE) Error in readGenericHeader(fullname, columns = ...
mirna microarray written 8.8 years ago by Christian Ruckert170

Latest awards to Christian Ruckert

Popular Question 2.6 years ago, created a question with more than 1,000 views. For rtracklayer bed import
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Unambiguously mapping of affy IDs to gene symbols using hgu133plus2.db

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