User: Cian Murphy

gravatar for Cian Murphy
Cian Murphy40
Reputation:
40
Status:
New User
Location:
United Kingdom
Last seen:
8 months, 3 weeks ago
Joined:
4 years, 3 months ago
Email:
c*************@ucl.ac.uk

Posts by Cian Murphy

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Error in Gviz | IdeogramTrack
... I tried the subversion and the error is still there.  ...
written 9 months ago by Cian Murphy40
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Comment: A: Error in Gviz | IdeogramTrack
... Any update on a fix for this?  ...
written 9 months ago by Cian Murphy40
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Get data frame of CNV calls from Seglist object
... I used runDNAcopy and then merged states to give me my seglist object:    > class(dat) [1] "SegList" attr(,"package") [1] "snapCGH" > ls(dat) [1] "genes" "method" "M.observed" "M.predicted" "num.states" "state" > It plots the graphs fine, with segmentation lines and all. Wh ...
dnacopy snapcgh seglist written 2.3 years ago by Cian Murphy40
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aCGH telling me to run find.hmm.states before merge hmm.states even though I have.
... I have run find.hmm.states by: aCGH.hmm <- find.hmm.states(aCGH) on an aCGH object. That seems to run fine as it displays its processing of each chromosome for every sample. I follow it with hmm.merged(aCGH.hmm) <- mergeHmmStates(aCGH.hmm) as per the manual. This nomenclature looks strange ...
acgh written 4.2 years ago by Cian Murphy40 • updated 4.2 years ago by Dan Du210
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Chr Info for array CGH - agilent 60K
... Hello, I have 60k Agilent array CGH data in the form of .txt and batch processed .cgh files. Neither appear readily import-able into R as there are no columns devoted entirely to Chr and Position. The .txt files have this info in columns interspersed with rows with things like "DarkCorner", or "HsC ...
cgh written 4.2 years ago by Cian Murphy40
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SKAT package on CRAN
... I'm attempting to run SKAT for the gene based tests. For the null model section, the code is: obj <-SKAT_Null_Model(phenotype ~ covariates_matrix, out_type="D") where phenotype is a numeric binary of 0/1 for case/control status. Does it matter if 0 is case or control and vice versa? Secondly, ...
written 4.3 years ago by Cian Murphy40 • updated 4.3 years ago by Dan Tenenbaum ♦♦ 8.2k

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