## User: twtoal

twtoal0
Reputation:
0
Status:
New User
Location:
Last seen:
2 days, 15 hours ago
Joined:
7 months, 2 weeks ago
Email:
t*****@ucdavis.edu

#### Posts by twtoal

<prev • 58 results • page 1 of 6 • next >
1
48
views
1
... In my PureCN results I see with most samples that there will be long stretches of the genome, e.g. many separate chromosomes, where the copy ratio (2 ^ log ratio) is approximately but not exactly 1, such as for example 1.02, 1.03, 0.98.  Typically the number is consistent in any given sample, perhap ...
written 4 weeks ago by twtoal0 • updated 4 weeks ago by markus.riester110
1
78
views
1
written 5 weeks ago by twtoal0
1
78
views
1
... Does the following seem like a good method to assign a p-value for segment DUPLICATION or DELETION, to each segment in the dnacopy.seg file? 1. Use PureCN's readCurationFile to read the .rds file into object RDS, then retrieve the log ratios of the marks in RDS$input$log.ratio 2. Compute the adjus ...
written 5 weeks ago by twtoal0
1
57
views
1
... What would you recommend regarding how to choose two thresholds (LO, HI) for adjusted copy ratio (CR), such that CR < LO is called a deletion and CR > HI is called a duplication?   ...
written 5 weeks ago by twtoal0 • updated 5 weeks ago by markus.riester110
2
61
views
2
... Okay, I'm just working on some reorganization to my pipeline.  I've decided to duplicate all the PureCN.R output files, one set prior to manual curation and the second after it.  I think I'll run Dx.R on the manually curated output, no need to run it on the initial output.   ...
written 6 weeks ago by twtoal0
2
61
views
2
... Is the mutation burden file produced by Dx.R affected at all by the purity/ploidy selection in the manual curation .csv file?   ...
written 6 weeks ago by twtoal0
1
57
views
1
... I have a case where the heatmap of PureCN optimal purity/ploidy solutions for a sample shows the maximum likelihood solution (marked with a 1 on the heatmap) is located at what appears to NOT be a heatmap peak.  I examined the heatmap numbers (used PureCN:::.matrixTotalPloidyToTumorPloidy() to get t ...
written 6 weeks ago by twtoal0
1
72
views
1
Comment: C: CNV in Normal Samples?
... Ok.  It would be very nice to be able to use PureCN for the germline too, for consistency's sake if nothing else.  Leaving the normal out of the pool would require making a separate pool file for each normal.  It would be nice if there were a way to tell PureCN to ignore a particular sample in the p ...
written 7 weeks ago by twtoal0
1
72
views
1
... Can PureCN be used to call CNVs in normal germline samples, using the pool of normals database to provide a standard normal reference?   ...
written 7 weeks ago by twtoal0 • updated 7 weeks ago by markus.riester110
1
94
views
1
... If I edit the manual curation file and change the purity and ploidy, is there any way to later on revert it back to the original PureCN-chosen solution's purity and ploidy (assuming I don't have a record of what that original purity and ploidy were)? Would this be correct?: > res = readRDS(samp ...
written 12 weeks ago by twtoal0 • updated 12 weeks ago by markus.riester110

#### Latest awards to twtoal

No awards yet. Soon to come :-)

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.