The UMI4Cats package provides functions for the pre-processing, analysis and visualization of UMI-4C chromatin contact data.
There are two different functions that can be used to prepare the files for analyzing them with UMI4Cats:
demultiplexFastq. Demultiplex reads belonging to
different viewpoints from a paired-end FastQ file.
digestGenome. Digest the reference genome of choice
using a given restriction sequence.
The pre-processing functions are wrapped in the contactsUMI4C
main function. This function will sequentially run the following steps:
prepUMI4C. Filter specific and high quality reads.
splitUMI4C. Split reads by the restriction sequence.
alignmentUMI4C. Align reads to the reference genome.
counterUMI4C. Apply UMI counting algorithm to quantify
the interactions with the viewpoint.
The statistics from the samples analyzed with the contactsUMI4C
function can be extracted and visualized with the function
statsUMI4C.
The analysis of UMI-4C data is wrapped in the construction of an object of
UMI4C class by the creator function makeUMI4C.
This function will group your samples according to the variable you provided
in the grouping argument (default: "condition") and then normalize it
to ref_umi4c.
Significant interactions with the viewpoint can be called when several
replicates are available, using the callInteractions function.
A set of query_regions, such as enhancers or open chromatin regions
needs to be provided. When no candidate regions are available, one can use
the function makeWindowFragments to join a fixed number of
restriction fragments into windows. The results of this analysis can be
visualized using plotInteractionsUMI4C and the list of
significant interactions can be retrieved using
getSignInteractions.
The differential analysis can be performed with
fisherUMI4C or waldUMI4C functions and can be
focused in a set of regions of interest by providing the query_regions
argument. Both will return a UMI4C object containing the
results of the differential test. You can access these results with the
method resultsUMI4C.
An integrative plot showing the results stored inside the UMI4C
object can be generated with the function plotUMI4C.