Chris,
Thanks for your kind comment!
The following code snippets should do.
FeatureIDs = annotatedPeak[!is.na(annotatedPeak$distancetoFeature) &
abs(annotatedPeak$distancetoFeature<5000000),]$feature
library(org.Hs.eg.db)
EnrichedGO = GetEnrichedGO(featureIDs, orgAnn="org.Hs.eg.db",
maxP=0.01, multiAdj=FALSE, minGOterm=10, multiAdjMethod="")
Best regards,
Julie
On 1/20/11 3:13 PM, "Christopher Ricupero" <ricupero@eden.rutgers.edu>
wrote:
Hello Dr. Zhu,
I have recently been introduced to your ChIPpeakAnno package and think
it is great.
However, I am having some difficulties when working with the
RangedData dataset once it is convereted and then annotated.
I followed your manuscript and exported the annotated Peak file into
excel, but I would like to do something different.
What I am trying to accomplish is to filter the annotated peak Ranged
Data by either the distancetoFeature or shortestDistance
variables. I am only interested in peaks that are very close to the
promoter regions and TSS so I wanted to limit these distances by
approx 5000 kb. After this , I would then run the GO analysis.
Is this possible to select on this variable to get a subset of my
annotated peaks before I run the enrichedGo function?
Thank you,
Chris
Christopher Ricupero
Graduate Fellow
Rutgers Univeristy
Piscataway, NJ 08854
[[alternative HTML version deleted]]
Chris,
Please type helpis.na) in a R session to access the menu about is.na
function. Please use & for and, | for or inside the [ ] for combining
selection criteria. The online book at
http://cran.r-project.org/doc/manuals/R-intro.pdf is a very useful
resource, it helped me a lot when I started.
FeatureIDs = annotatedPeak[!is.na(annotatedPeak$distancetoFeature) &
abs(annotatedPeak$distancetoFeature<5000000) & annotatedPeak$
insideFeature %in% c("upstream" , "inside" , "overlapStart"),]$feature
Best regards,
Julie
On 1/20/11 4:52 PM, "Christopher Ricupero" <ricupero@eden.rutgers.edu>
wrote:
Hi Julie
Thanks for the quick reply. Could I potentially bother you one more
time. If you could send me some info on how to manipulate the ranged
data that would be great.
This function did work, but I wanted to take it 1 step further: To
take only (5000 upstream, inside, overlap) and limit to only (500 bp
downstream)
My questions are:
1. What is the [!is.na mean?
2. I would like to combine my arguments. Instead of taking just
the absolute value of 50000000 in distance to feature. I would like to
take 50000 distance to feature plus insideFeature : upstream, inside,
overlapStart, etc.. but then only 500 bp downsteam. I am sure there
is a way to do this, I am just unsure of the syntax and how to combine
the arguments.
Could I say something like :
abs(annotatedPeak$distancetoFeature<5000000) and annotatedPeak$
insideFeature=upstream, inside, overlapStart)]?
Thanks, Chris
From: Zhu, Lihua (Julie) [mailto:Julie.Zhu@umassmed.edu]
Sent: Thursday, January 20, 2011 3:36 PM
To: Christopher Ricupero; Ou, Jianhong
Cc: bioconductor@stat.math.ethz.ch
Subject: Re: ChIPpeak Anno RangedData question
Chris,
Thanks for your kind comment!
The following code snippets should do.
FeatureIDs = annotatedPeak[!is.na(annotatedPeak$distancetoFeature) &
abs(annotatedPeak$distancetoFeature<5000000),]$feature
library(org.Hs.eg.db)
EnrichedGO = GetEnrichedGO(featureIDs, orgAnn="org.Hs.eg.db",
maxP=0.01, multiAdj=FALSE, minGOterm=10, multiAdjMethod="")
Best regards,
Julie
On 1/20/11 3:13 PM, "Christopher Ricupero" <ricupero@eden.rutgers.edu>
wrote:
Hello Dr. Zhu,
I have recently been introduced to your ChIPpeakAnno package and think
it is great.
However, I am having some difficulties when working with the
RangedData dataset once it is convereted and then annotated.
I followed your manuscript and exported the annotated Peak file into
excel, but I would like to do something different.
What I am trying to accomplish is to filter the annotated peak Ranged
Data by either the distancetoFeature or shortestDistance
variables. I am only interested in peaks that are very close to the
promoter regions and TSS so I wanted to limit these distances by
approx 5000 kb. After this , I would then run the GO analysis.
Is this possible to select on this variable to get a subset of my
annotated peaks before I run the enrichedGo function?
Thank you,
Chris
Christopher Ricupero
Graduate Fellow
Rutgers Univeristy
Piscataway, NJ 08854
[[alternative HTML version deleted]]