## User: rafa

rafa60
Reputation:
60
Status:
Trusted
Location:
United States
Last seen:
1 year, 9 months ago
Joined:
3 years, 10 months ago
Email:
r***@jimmy.harvard.edu

#### Posts by rafa

<prev • 5 results • page 1 of 1 • next >
1
854
views
1
... 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 21 months ago by rafa60
0
484
views
0
... 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. ...
written 3.0 years ago by rafa60
0
822
views
0
... 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 ...
written 3.9 years ago by rafa60 • updated 3.9 years ago by Michael Love19k
4
1.2k
views
4
... Hi I updated all this. I will make a general announcement. ...
written 3.9 years ago by rafa60
3
902
views
3
... 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 3.9 years ago by rafa60

#### Latest awards to rafa

No awards yet. Soon to come :-)

Content
Help
Access

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