User: graggsd

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graggsd0
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Posts by graggsd

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Bumphunter Algorithm Returns Regions with very few CpGs
... Topic: I have a question related to the appropriateness of making a slight modification to the `bumphunter` function for my analysis. Scenario: I have an Illumina 450K dataset that has been QC'd and normalized implementing the `minfi` package and have used the `bumphunter` function to search for DM ...
minfi bumphunter written 13 months ago by graggsd0
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Highlighting Significantly Associated Sites on Manhattan Plot using ggbio
... Hi all, I'm experiencing difficulty implementing the highlight.gr argument within the plotGrandlinear function of ggbio. I'm trying to highlight and label significant sites from an association study. I can produce a manhattan plot, but cannot seem to get my significant points highlighted and labele ...
ggbio manhattan plot plotgrandlinear written 15 months ago by graggsd0
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Comment: C: Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of
... Regarding the way GOstats implements the hypergeometric test, I actually wasn't aware that it propagated inherited terms back through the DAG. However, since I'm looking at data from 450K arrays, I decided to implement the "gometh" function from missMethyl since it will take lists of "significant" a ...
written 15 months ago by graggsd0
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Gene Ontology Overrepresentation Analysis with a custom level of Abstraction of GO Terminology
... I want to perform an overrepresentation for GO terms for a particular microarray experiment. Most of the methods to do this in R (see the "gometh" function included in the missMethyl package or "hyperGTest" in the GOstats package) only consider a test for enrichment of terms directly annotated by a ...
go gostats gene ontology missmethyl overrepresentation analysis written 15 months ago by graggsd0 • updated 15 months ago by James W. MacDonald45k

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