User: jcarter

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jcarter0
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Posts by jcarter

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Comment: C: Preparing CopywriteR output for GISTIC 2.0 analysis
... Thank you! I took out the floor function for the markers part since it was causing a mismatch error in GISTIC (secondary to my segmentation_values start positions ending in ".5"), but after that it ran perfectly! ...
written 20 months ago by jcarter0
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Preparing CopywriteR output for GISTIC 2.0 analysis
... I'm interested in looking for recurrent somatic copy number aberrations (RCNAs) amongst the CNVs detected by CopywriteR using GISTIC 2.0 (which is arguably the standard tool used for identifying RCNAs). As per the GISTIC 2.0 documentation ( ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTICDocumentat ...
copywriter written 20 months ago by jcarter0 • updated 20 months ago by t.kuilman100
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Comment: C: Visualizing CopywriteR's segmentation output in IGV
... PERFECT! That is exactly what happened! Fixed it with a  segment.CNA.object$output$chrom <- paste("chr",segment.CNA.object$output$chrom,sep="") Thank you so much! ...
written 21 months ago by jcarter0
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Comment: C: Visualizing CopywriteR's segmentation output in IGV
... Thank you! I seem to be running into trouble at the seg.values part.  > seg.values <- lapply(segments, function(x, bins) { + ## Create GRanges object + x <- x[, c("chrom", "loc.start", "loc.end", "seg.mean")] + colnames(x) <- c("Seqnames", "Start", "End", "Segmean") + x[, "Star ...
written 21 months ago by jcarter0
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Comment: C: Calling amplifications and deletions from CopywriteR output
... Done! :) https://support.bioconductor.org/p/78926/ ...
written 21 months ago by jcarter0
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Visualizing CopywriteR's segmentation output in IGV
... Excellent tool! I'm interested in methods to convert the data within CopywriteR's segmentation output from DNAcopy, segment.CNA.object, to something that could be saved and visualized as an *.igv file (or any other IGV compatible file format)? (Similar to the *.igv file for the raw log2 transformed ...
dnacopy copywriter written 21 months ago by jcarter0 • updated 21 months ago by t.kuilman100
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Comment: C: Calling amplifications and deletions from CopywriteR output
... Excellent tool! And this thread is extremely helpful! On a similar note as the previous inquiry, would you be able to offer guidance on how one could convert the data within segment.CNA.object to something that could be saved and visualized as a *.igv file (or any other IGV compatible file format)? ...
written 21 months ago by jcarter0

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