User: pertille

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pertille0
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Posts by pertille

<prev • 21 results • page 1 of 3 • next >
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Comment: C: How to represent a relationship between physical map and linkage map of a sequen
... Thank you very much you have missed a "(" in this sentence (I have no reputation enough to edit): seg.f <- data.frameseg.name=segs, seg.Start=start, seg.End=end,                      the.v=runif(length(end)), Note=sample(LETTERS, length(end), rep=T)); ...
written 20 months ago by pertille0
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How to represent a relationship between physical map and linkage map of a sequenced data using OmicCircos or another similar
... We wanna do a graph to show the Syntenic links between a linkage map and physical map visualized using Circos source("http://bioconductor.org/biocLite.R") biocLite("OmicCircos") Each line will represents a connection between the position of a particular marker in our linkage map (black; scale in ...
omiccircos linkage disequilibrium bioconductor for genomic data science software r written 20 months ago by pertille0 • updated 20 months ago by Hu, Ying NIH/NCI [E]50
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I can not create the HeatMap chart on DEseq2
... I am trying to do a heatmap using this pipeline: http://bio.biomedicine.gu.se/~marcela/courses/2014/imbi/practicals/4-RNASeq.html Everything works well except the "heatmap.2" graph I think that it is a problem with the object: "sig2heatmap", that is generated by: assay(rld)[rownames(assay(rld))% ...
deseq2 R written 21 months ago by pertille0 • updated 21 months ago by Michael Love14k
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How to do FDR p.adj manually on "mr.edgeR object" from MEDIPS package?
... As I am working with a reduced-genome and the "p.adj" take in account all the  windows in the genome, this filter is eliminating all of my windows with differential methylation profile: Using this command in MEDIPS package, I can do my differencial methylation analysis including de FDR correction a ...
edger medips R written 21 months ago by pertille0 • updated 21 months ago by Lukas Chavez470
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Error in MEDIPS.calibrationCurve looking for different methylation profiles
... I am looking for different methylation profile between two different environmental conditions(control[MeDIP_C] and test(MeDIP_AV) in chickens. I also have a input that is a reduced genome sequencing from the same specie used in this experiment, but without methylation enrichment (I am not sure if I ...
medips R written 21 months ago by pertille0 • updated 21 months ago by Lukas Chavez470
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How createSet from reduced "paire-ed" sequencing on MeDIPS?
... I'm trying to create a set with my .BAM file that was generated from reduced "paired end" sequencing (using restriction enzyme), I can easily run it as "single end", but when I add "paired = T" in the command, this message appears: > MeDIP_RJF_AV163=MEDIPS.createSet(file=RJF_AV163, BSgenome=gen ...
medips R input files written 21 months ago by pertille0 • updated 21 months ago by Lukas Chavez470
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(Closed) How createSet from reduced "paire-ed" sequencing on MeDIPS?
... I'm trying to create a set with my .BAM file that was generated from reduced "paired end" sequencing (using restriction enzyme), I can easily run it as "single end", but when I add "paired = T" in the command, this message appears: > MeDIP_RJF_AV163=MEDIPS.createSet(file=RJF_AV163, BSgenome=gen ...
medips R input files written 21 months ago by pertille0
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Comment: C: How can I extract sequences from a FASTA file for each of the intervals defined
... Thank you @Martin Do you know why this error? The command looks like correct according to the manual: http://finzi.psych.upenn.edu/library/GenomicRanges/html/GRanges-class.html > genomerngs = as(seqinfo(BSgenome.Ggallus.UCSC.galGal4, "GRanges")) Error in .identC(Class, "double") :   argument "C ...
written 21 months ago by pertille0
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Comment: C: How can I extract sequences from a FASTA file for each of the intervals defined
... Thank you @Martin Morgan, the problem is that when I run this command: {seq = BSgenome::getSeq(BSgenome.Ggallus.UCSC.galGal4, olaps)} The follow error message appear: Error in loadFUN(x, seqname, ranges) :   trying to load regions beyond the boundaries of non-circular sequence "chr4" What is we ...
written 21 months ago by pertille0
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How can I extract sequences from a FASTA file for each of the intervals defined in a BED file using R?
... How can I extract sequences from a FASTA file for each of the intervals defined in a BED file using R? The reference genome used is "Gallus gallus" that can be obtained by: source("http://bioconductor.org/biocLite.R") biocLite("BSgenome.Ggallus.UCSC.galGal4") library(BSgenome.Ggall ...
granges R bioconductor written 21 months ago by pertille0

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