atacr
ObjectWhen make_counts()
is run, an atacr
object is returned. This is a simple, somewhat informal object based on the R list type. It is basically an R list with the following members:
GenomicRanges::Granges
object describing the bait window regions RangedSummarizedExperiment
object containing the counts in the windows in bait_regions
RangedSummarizedExperiment
object containing the counts in the windows in the regoions outside bait_regions
as.data.frame()
on the atacr
objectThe RangedSummarizedExperiment
objects carry the count data. They are organised as a matrix with rows representing windows and columns different samples. Their order is conserved and is the same as that in the treatments
, samples
and bam_files
.
Many of the functions allow you to state which member of the atacr
list (really a RangedSummarizedExperiment
) you wish to apply the function to with the which
argument, e.g
plot_counts(counts, which = "bait_windows", log10 = FALSE)
atacr
objectIn this way you can use functions that return RangedSummarizedExperiment
s to become new members in the list and work on them as with the built in ones, this is especially useful for normalisations.
counts$by_sample <- library_size_normalisation(counts, by_treatment = TRUE) plot_counts(counts, which = "by_sample", log10 = FALSE)
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