Run_NxtIRF_Filters {NxtIRFcore} | R Documentation |
This function implements filtering of IR or AS events based on customisable criteria. See NxtFilter for details.
get_default_filters() apply_filters(se, filters = get_default_filters()) runFilter(se, filterObj)
se |
the NxtSE object to filter |
filters |
A vector or list of one or more NxtFilter objects. If left blank, the NxtIRF default filters will be used. |
filterObj |
A single NxtFilter object. |
We highly recommend using the default filters, which are as follows:
(1) Depth filter of 20,
(2) Coverage filter requiring 90% coverage in IR events.
(3) Coverage filter requiring 60% coverage in AS events (i.e. Included + Excluded isoforms must cover at least 60% of all junction events across the given region)
(4) Consistency filter requring log difference of 2 (for skipped exon and mutually exclusive exon events, each junction must comprise at least 1/(2^2) = 1/4 of all reads associated with each isoform). For retained introns, the exon-intron overhangs must not differ by 1/4
In all filters, we require at least 80% samples (pcTRUE = 80
)
to pass this filters from the entire dataset (minCond = -1
).
Events with event read depth (reads supporting either included or excluded
isoforms) lower than 5 (minDepth = 5
) are not assessed in filter #2, and
in #3 and #4 this threshold is (minDepth = 20
).
For an explanation of the various parameters mentioned here, see NxtFilter
For runFilter
and apply_filters
: a vector of type logical
,
representing the rows of NxtSE that should be kept.
For get_default_filters
: returns a list of default recommended filters
that should be parsed into apply_filters
.
get_default_filters
: Returns a vector of recommended default
NxtIRF filters
apply_filters
: Run a vector or list of NxtFilter objects
on a NxtSE object
runFilter
: Run a single filter on a NxtSE object
NxtFilter for details describing how to create and assign settings to NxtFilter objects.
# see ?MakeSE on example code of how this object was generated se <- NxtIRF_example_NxtSE() # Get the list of NxtIRF recommended filters filters <- get_default_filters() # View a description of what these filters do: filters # Filter the NxtSE using the first default filter ("Depth") se.depthfilter <- se[runFilter(se, filters[[1]]), ] # Filter the NxtSE using all four default filters se.defaultFiltered <- se[apply_filters(se, get_default_filters()), ]