You're rigth, I move to the BioC list.
I tried your exemple, it works well.
In the exptData, do I really need all these fields ? or can I use an empty string for projectPath, fragmentDir, reSequence1 ... ?
Then, just to clarify some points ;
fc@colData is your experimental design, so in your exemple, you have 6 samples from the same viewpoint "testdata".
What about rowData ? if I'm correct, these are the measures (counts) per viewpoint ? so here you only have interacting loci per viewpoint ? Which make sense with the dim of the counts object (6 samples x 2 measures)
I'm just wondering if you can have multiple viewpoints in the same FourC object ? with potentially different number of measures ...
Thank you again,
this might be interesting to other users as well. So I would recommend we move the discussion to the Biocondoctor Support Forum if this is fine with you.
Have a look at the script below. This should explain all the steps you need to do to add a custom fragment reference, viewpoint information and counts.
exptData <- SimpleList(projectPath=tempdir(),
colData <- DataFrame(viewpoint = "testdata",
condition = factor(rep(c("WE_68h", "MESO_68h", "WE_34h"),
levels = c("WE_68h", "MESO_68h", "WE_34h")),
replicate = rep(c(1, 2),
bamFile = "",
fc <- FourC(colData, exptData)
## this step can also be skipped by adding your fragment reference (GRanges)
##rowData(fc) <- your Fragment GRanges
fc <- addFragments(fc)
## counts would by your HiC counts, here I take a random sample
cnts <- matrix(sample(1:10, prod(dim(fc)), replace = TRUE),
## make sure they are integers otherwise you will get an error
counts(fc) <- cnts
## manually add viewpoint information because there is no primerfile
colData(fc)$chr = "chr2L"
colData(fc)$start = 6027
colData(fc)$end = 6878
## now you should be able to continue with the workflow
On 10/09/2015 06:34 PM, Nicolas Servant wrote:
I'm developing the HiTC package on Bioconductor to analyse Hi-C data.
I would like to make a test to see whether the method implemented in FourCSeq can be used on some specific Hi-C viewpoints (so 4C like information).
So actually, my question is quite simple, let's say that I have a GRanges objects with a count information extracted from HiTC, and that I would like to enter into FourCSeq to detect valid interactions.
I saw that the FourC object require many information about the pre-processing such as the BAM file, etc.
Could give any advices to create such object from a count table ?
Thank you very much