User: Hermann Norpois

gravatar for Hermann Norpois
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Germany
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4 years, 7 months ago
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Posts by Hermann Norpois

<prev • 19 results • page 1 of 2 • next >
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Answer: A: GRanges - changing seqlevels
... Hm ... Yes, it helps ... Actually it was a typo 'ch8' instead of 'chr8'. Many thanks.     ...
written 4.6 years ago by Hermann Norpois170
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GRanges - changing seqlevels
... Hello, I am not able to change seqlevels (as I think I was used to) for GRanges objects. seqlevels (gr) <- seqlevels (noexons1) Fehler in getDanglingSeqlevels(x, new2old = new2old, force = force, seqlevels(value)): won't drop seqlevels currently in use (ch8), unless you use 'force=TRUE' to als ...
seqlevels granges written 4.6 years ago by Hermann Norpois170
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Answer: Re: Repeat masker sequences as GRanges object
... Thanks, I followed your instructions but I got an error message: library (AnnotationHub) > hub <- AnnotationHub() > seq.masked <- hub$goldenpath.hg19.database.rmsk_0.0.1.RData Retrieving ‘goldenpath/hg19/database/rmsk_0.0.1.RData’ Fehler: Lesefehler aus Verbindung # 'Fehler' means erro ...
written 5.2 years ago by Hermann Norpois170
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Answer: A: Repeat masker sequences as GRanges object
... I continued ... active (masks (ch1))["AMP"] <- FALSE masks (ch1) MaskCollection of length 4 and width 249250621 masks: maskedwidth maskedratio active names desc 1 23970000 0.09616827 FALSE AGAPS assembly gaps 2 0 0.00000000 TRUE AMB intra-contig am ...
written 5.2 years ago by Hermann Norpois170
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Repeat masker sequences as GRanges object
... Hello, I would like to have repeat sequences as GRanges object I started with ... library (BSgenome.Hsapiens.UCSC.hg19) ch1 <- Hsapiens$chr1 active (masks (ch1)) AGAPS AMB RM TRF TRUE TRUE FALSE FALSE active (masks(ch1))["RM"] <- TRUE active (masks (ch1)) AGAPS AMB RM TRF TR ...
written 5.3 years ago by Hermann Norpois170
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simulating genetic data
... Hello, I am looking for a tool that simulates gwa-data for a quantitative trait. I would like to have a matrix with 0,1,2 for the number of minor allels for about 200000 snps (e.g. in columns) and the phenotypes (the quantitative trait) in rows. Can anybody give me a hint? Thanks Hermann [ ...
written 6.2 years ago by Hermann Norpois170 • updated 6.2 years ago by James W. MacDonald52k
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Order within a GRanges object
... Hello, I have some points according to the internal order of granges objects. 1) Automatically there is an order depending on the a) seqnames (= chromosomes) and b) the ranges. 2) The seqnames are always sorted in ascii order. 3) After df <- as.data.frame m <- regexpr ("\\d+", df$s ...
written 6.3 years ago by Hermann Norpois170 • updated 6.3 years ago by Malcolm Cook1.5k
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GRange - append metadata from a dataframe
... Hello, I have a dataframe df1 and a grange object gr. The rownames respectively names (gr) are identical but not necessary in the same order. I wish to append df1 as metadata to the gr (of course rownames (df) and names (gr) must fit). Could you please give me a hint. Thanks Hermann > df1 ...
written 6.4 years ago by Hermann Norpois170 • updated 6.4 years ago by Michael Lawrence11k
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transform gwaa.data (Genabel) to snp.matrix (chopsticks)
... Hello, is there a way to transform a gwaa.data-object (from Genabel) to an object of class snp.matrix (from chopsticks)? Thanks Hermann [[alternative HTML version deleted]] ...
snp written 6.7 years ago by Hermann Norpois170 • updated 6.7 years ago by Paul Geeleher1.3k
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Granges: range (gr) does not function
... Hello, I recognised a strange behaviour of range (gr). Shouldnt it treat the whole grange object? Like ranges(gr)? But it doesnt. What's wrong? Thanks Hermann > gr GRanges with 4 ranges and 1 metadata column: seqnames ranges strand | score | ...
written 6.7 years ago by Hermann Norpois170 • updated 6.7 years ago by Hervé Pagès ♦♦ 14k

Latest awards to Hermann Norpois

Popular Question 4.6 years ago, created a question with more than 1,000 views. For Repeat masker sequences as GRanges object
Popular Question 4.6 years ago, created a question with more than 1,000 views. For subset GRanges object via ElementMetadata
Popular Question 4.6 years ago, created a question with more than 1,000 views. For GRange - append metadata from a dataframe
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Order within a GRanges object
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Generate a GRangesList from a classical list of GRangesObjects
Popular Question 4.6 years ago, created a question with more than 1,000 views. For GRanges - changing seqlevels

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