User: rbronste

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rbronste20
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@RBronshteyn
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Posts by rbronste

<prev • 64 results • page 1 of 7 • next >
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Comment: C: Filtering DESeq2 result export along multiple lines
... So I am just trying to compile a list of DE peaks where for instance LFC < -2 would be considered treatment enhanced and LFC > 2 would be vehicle enhanced. With those between the two LFC values being considered as shared.  ...
written 3 days ago by rbronste20
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Comment: C: Filtering DESeq2 result export along multiple lines
... So I am actually doing this with converted ChIP-seq counts representing a vehicle or treatment condition, so thought there may be a more nuanced method of approaching those with:  lfcThreshold ...
written 3 days ago by rbronste20
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Comment: C: Filtering DESeq2 result export along multiple lines
... So something along these lines: resLFC <- results(dds, lfcThreshold = 2, altHypothesis = "greaterAbs") However one question I have, maybe Im missing something but this is from the vignette:  Two arguments to the results function allow for threshold-based Wald tests: lfcThreshold, which takes ...
written 3 days ago by rbronste20
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Filtering DESeq2 result export along multiple lines
... Wondering if there is a way to filter the following output: resOrdered <- res[(res$padj < 0.01),] write.csv(as.data.frame(resOrdered$padj < 0.01),file="test.csv") so as to get as an output .csv only (something below a padj, with a fold-change cutoff, as well as a minimum baseMean) simult ...
deseq deseq2 differential binding analysis written 3 days ago by rbronste20 • updated 3 days ago by Michael Love14k
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Comment: C: Cleaning up DiffBind counts in relation to chromosome map
... Thanks, exactly what I needed! ...
written 4 days ago by rbronste20
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Cleaning up DiffBind counts in relation to chromosome map
... Wondering how I can go about outputting the following command which would have the chromosome map already applied? So for instance instead of "chromosome # 26" representing the X, it is already changed in the binding matrix following counting, or is this only possible in post-processing (e.g. editin ...
chipseq diffbind differential binding analysis written 4 days ago by rbronste20 • updated 4 days ago by Rory Stark2.1k
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Removing/combining specific annotation categories in ChIPSeeker plots/analysis
... Running the following code: peakAnno <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000), TxDb=TxDb.Mmusculus.UCSC.mm10.knownGene, annoDb="org.Mm.eg.db") plotAnnoBar(peakAnnoList, title = "MeA F/M Peak Annotation") In the current form plotting 11 annotation categorie ...
chipseq annotation chipseeker written 5 days ago by rbronste20
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Comment: C: Unable to find an inherited method for function distanceToNearest for signature
... > sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.4 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Framew ...
written 5 days ago by rbronste20
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Comment: C: Altering design following DESeqDataSetFromMatrix and DESeq
... Great thanks thats what I was looking for! I guess then my original point holds true, that to test DE wrt one covariate or the reverse, you just need two independent designs and results tables? I probably did not make that too clear in my original question.  ...
written 5 days ago by rbronste20
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Comment: C: Unable to find an inherited method for function distanceToNearest for signature
... data(peaks_E2F4, package = 'chipenrich.data') chipenrich(peaks_E2F4, genome = 'hg19', genesets = c('GOBP', 'GOCC', 'GOMF'), locusdef = "nearest_tss", qc_plots = FALSE, out_name = NULL, n_cores = 1) And getting the following error: Reading peaks from data.frame.. Constructing GRanges Sorting GR ...
written 5 days ago by rbronste20

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