User: jcarter

gravatar for jcarter
jcarter0
Reputation:
0
Status:
New User
Location:
Last seen:
2 years, 7 months ago
Joined:
2 years, 7 months ago
Email:
j******@path.wustl.edu

Posts by jcarter

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answers
1.4k
views
1
answers
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 2.6 years ago by jcarter0
1
vote
1
answer
1.4k
views
1
answer
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 2.6 years ago by jcarter0 • updated 2.6 years ago by t.kuilman140
0
votes
1
answers
972
views
1
answers
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 2.6 years ago by jcarter0
0
votes
1
answers
972
views
1
answers
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 2.6 years ago by jcarter0
0
votes
3
answers
884
views
3
answers
Comment: C: Calling amplifications and deletions from CopywriteR output
... Done! :) https://support.bioconductor.org/p/78926/ ...
written 2.6 years ago by jcarter0
2
votes
1
answer
972
views
1
answer
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 2.6 years ago by jcarter0 • updated 2.6 years ago by t.kuilman140
0
votes
3
answers
884
views
3
answers
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 2.6 years ago by jcarter0

Latest awards to jcarter

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 370 users visited in the last hour