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Go here to look at it in the genome browser - see anything interesting? |
We can also open R interactively to look at the contents of the big "seekOutput.RData" file we made. We need to use the R set up by the BioITeam, rather than the one in the module system, so we can use a version 3.x. These are a possible sequence of commands:
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cd $SCRATCH/ripseq_exercises/CLIP/
$BI/bin/R
#Now we are in R
library(RIPSeeker, lib.loc="./lib")
rip_data = load("seekOutput.RData")
rip
# [1] "mainSeekOutputRIP" "RIPGRList" "mainSeekOutputCTL"
# [4] "annotatedRIPGR" |
Here, "rip_data" is a list of four objects that we just loaded into R, and each contains different sub-objects and information.
| Object | Component Objects | Information Content |
|---|---|---|
| mainSeekOutputRIP | nbhGRList alignGal alignGalFiltered | Information such as the HMM posterior probabilities and filtered alignment objects for the RIP sample |
| RIPGRList | a GRangesList | A list (in GRanges object form) of all peak regions called by RIPSeeker |
| mainSeekOutputCTL | nbhGRList alignGal alignGalFiltered | Information such as the HMM posterior probabilities and filtered alignment objects for the CTL sample |
| annotatedRIPGR | sigGRangesAnnotated enrichedGO | Annotations for each of the regions flagged in RIPGRList, as well as calling of significantly enriched GO terms for those regions; this only works if "ChIPpeakAnno" is loaded and you set the functions biomaRt, biomaRt_dataset, and goAnno (see below) |
Alternatives
We could have added these lines to the ripseeker_script.R file:
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