Entering edit mode
leehami7407
•
0
@leehami7407-24156
Last seen 4.2 years ago
Hello, I am currently using CAGEr to analyze CAGE data from Fantom5. I put human fetal brain and human adult brain data set.
cumulativeCTSSdistribution(adultbrainx1, clusters = "tagClusters")
quantilePositions(adultbrainx1, clusters = "tagClusters", qLow = 0.1, qUp = 0.9)
##to get tag clusters and their interquantile width##
tagClustersGR( adultbrainx1, "fetalbrain_reformat_x.bed"
, returnInterquantileWidth = TRUE, qLow = 0.1, qUp = 0.9)
tagClustersGR( adultbrainx1, "adultbrain_reformat_x.bed"
, returnInterquantileWidth = TRUE, qLow = 0.1, qUp = 0.9)
plotInterquantileWidth(adultbrainx1, clusters = "tagClusters", tpmThreshold = 3, qLow = 0.1, qUp = 0.9)
After this, I only get one plot for fetalbrainreformatx.bed but not adultbrainreformatx.bed
Can I get a help for this?
Thank you,
Hello, is there a way you can share your CAGEr object with me?
sure bur how should I share it with you? do you think the object is the problem here?
I need to be able to reproduce the problem on my computer to work on it. The best for me would be if you could prepare a reproducible example with test data. But if this is difficult, I can have a look at your CAGEr object serialised with
saveRDS.I cant see your email address! Could you give me your email address? or is there any other ways to send you my file?
My email address is charles.plessy at oist dot jp (email addresses from package maintainers are listed on the package's page on the Bioconductor website and in the DESCRIPTION page of the package. If it is not too late, please feel free to send me a rds object.