User: rafa

gravatar for rafa
rafa60
Reputation:
60
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Location:
United States
Last seen:
10 months, 2 weeks ago
Joined:
2 years, 11 months ago
Email:
r***@jimmy.harvard.edu

Posts by rafa

<prev • 5 results • page 1 of 1 • next >
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Answer: A: bumphunter output clarification
... I would start by reading the Details section of the bumphunter help file.  Regarding the table, each row is a candidate DMR. value - is the average of the estimated coefficient (usually representing the difference between two groups) in the region area - is the absolute value of the sum of the es ...
written 10 months ago by rafa60
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News: Bug found and fixed in bumphunter's bootstrap method
... Andrew Jaffe found and fixed a bug in bumphunter's bootstrap method. The coefficient for which inference was performed was fixed at 2 (the default). This is now changed to the coefficient passed along as `coef` This has been fixed in version 1.9.3. ...
bumphunter news written 2.1 years ago by rafa60
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News: Changes to matchGenes in bumphunter
... The function matchGenes in the bumphunter package found the nearest gene/transcript to each entry in a GRanges and annotated with information such as if it is in an intron, exon, which exon, if it overlaps, covers or is inside, as well as with gene symbols, and refseq IDs. For historical reasons, th ...
annotation bumphunter news written 2.9 years ago by rafa60 • updated 2.9 years ago by Michael Love14k
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Answer: A: Using bumphunter with non-human genomes
... Hi I updated all this. I will make a general announcement. ...
written 2.9 years ago by rafa60
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Answer: A: bumphunter::annotateNearest with non-human genome
... Jessica, I've made some major changes to bumphunter to accommodate this. If you install the latest devel version 1.7.3 (still being tested) the matchGenes and annotateNearest will no longer assume hg19. Here is an example: library(bumphunter) islands=makeGRangesFromDataFrame(read.delim("http://raf ...
written 2.9 years ago by rafa60

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