User: rbronste

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rbronste60
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Posts by rbronste

<prev • 130 results • page 1 of 13 • next >
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Comment: C: Split AME .tsv file into GRanges object or DataFrame
... So after read.table, if I do as you suggest I get the following error: > gr<- GRanges(t$seq_ID) Error in .from_character_to_GRanges(from) : The character vector to convert to a GRanges object must contain strings of the form "chr:start-end" or "chr:start-end:strand", with end >=start - 1 ...
written 14 days ago by rbronste60
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Split AME .tsv file into GRanges object or DataFrame
... I have an AME motif calling output as follows (in a .tsv file) and can import this into R using read.table, however I would like to take the motif_ID, seq_ID, and class fields and split it off into a GRanges object or DataFrame, how can I go about doing this? Thanks! motif_DB ...
granges motif meme dataframe ame written 14 days ago by rbronste60 • updated 14 days ago by Michael Lawrence10k
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Comment: C: DESeq2 memory allocation question
... > sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.5 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Framework ...
written 23 days ago by rbronste60
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Comment: C: DESeq2 memory allocation question
... I am actually already doing this (135k in matrix after reduction), however following this command: dds <- DESeq(dds, betaPrior = TRUE, fitType = c("local"), parallel = TRUE) It tells me Im out of application memory right at the end of DESeq, sometimes even shutting off my computer. ...
written 23 days ago by rbronste60
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DESeq2 memory allocation question
... Looking to reallocate more application memory to DESeq2 because when running: betaPrior = TRUE On a large matrix, I run out of application memory. Anyone have ideas how to get around this on a Mac (Quad Core w/ 16gb RAM)? Thanks! ...
deseq2 memory problem written 23 days ago by rbronste60 • updated 23 days ago by Michael Love20k
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Comment: C: Subscript error from TSS proximity function
... Is  PACKAGE = "S4Vectors" not a Bioconductor package? ...
written 4 weeks ago by rbronste60
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(Closed) Subscript error from TSS proximity function
... Hi all,  Have a set of peaks and TSSs, trying to use the following function to retrieve the distance from peaks to nearest TSS and getting this error: Wondering you anyone has an idea about why? Thanks! # Get distance from peaks to the nearest TSS tmp <- getNearestDist(all.peaks,tss,return.ne ...
diffbind s4vectors function tss written 4 weeks ago by rbronste60 • updated 4 weeks ago by Michael Love20k
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Comment: C: DESeq2 group comparison
... Thanks for the info. I am fine sorting by the (adjusted) pvalue, Im moreso interested in matching the way I do the 4-way analysis here to the following which is what I am doing for straightforward pairwise comparisons (where I don't do the onesided lfcThreshold): table(sampleTreatment) dds<-DE ...
written 7 weeks ago by rbronste60
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DESeq2 group comparison
... Quick question about running some 4-way comparisons, have the following set up: table(sampleSex, sampleTreatment) dds<-DESeqDataSet(se, design= ~batch + sex + treatment) dds$group <- factor(paste0(dds$sex, dds$treatment)) design(dds) <- ~0 + group dds <- dds[ rowSums(counts(dds)) & ...
deseq deseq2 differential binding analysis written 7 weeks ago by rbronste60 • updated 7 weeks ago by Michael Love20k
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DESeq2 relevel still gives negative log2FoldChange
... Although I relevel in the following way, the GRanges with results still lists BB as the negative log2FoldChange, wondering what I am doing incorrectly here? Thanks. dds<-DESeqDataSet(se, design= ~batch + treatment) dds$group <- factor(paste0(dds$treatment)) dds$treatment<-relevel(dds$tr ...
deseq2 written 3 months ago by rbronste60 • updated 3 months ago by Michael Love20k

Latest awards to rbronste

Centurion 17 months ago, created 100 posts.
Supporter 17 months ago, voted at least 25 times.

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