Run_SpliceWiz_Filters: Filtering for IR and Alternative Splicing Events

In alexchwong/SpliceWiz: interactive analysis and visualization of alternative splicing in R

Filtering for IR and Alternative Splicing Events

Description

These function implements filtering of alternative splicing events, based on customisable criteria. See ASEFilter for details on how to construct SpliceWiz filters

Usage

getDefaultFilters()

applyFilters(se, filters = getDefaultFilters())

runFilter(se, filterObj)

Arguments

se	the NxtSE object to filter
filters	A vector or list of one or more ASEFilter objects. If left blank, the SpliceWiz default filters will be used.
filterObj	A single ASEFilter object.

Details

We highly recommend using the default filters, which are as follows:

• (1) Depth filter of 20,

• (2) Participation filter requiring 70% coverage in IR events.

• (3) Participation filter requiring 40% coverage in MXE, SE, A5SS and A3SS events (i.e. Included + Excluded isoforms must cover at least 40% 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

• (5) Terminus filter: In alternate first exons, the splice junction must not be shared with another transcript for which it is not its first intron. For alternative last exons, the splice junction must not be shared with another transcript for which it is not its last intron

• (6) ExclusiveMXE filter: For MXE events, the two alternate casette exons must not overlap in their genomic regions

• (7) StrictAltSS filter: For A5SS / A3SS events, the two alternate splice sites must not be interrupted by an intron

In all data-based filters, we require at least 80% samples (pcTRUE = 80) to pass this filters from the entire dataset (minCond = -1).

Threshold depths for Participation filters:

For IR/RI, Participation filter is only applied for IR events for which the intron depth is above a certain threshold (set by minDepth). This avoids the filters running on samples for which there is no IR.

For non-IR ASEs, Participation is only run on events with splice depth (SpliceOver metric) higher than minDepth. This avoids filters running on events with low total participation (i.e., (Inc+Exc)/SpliceOver)

Threshold depths for Consistency filters: Consistency filters are only applied for events where the sum of upstream and downstream junction counts surpass a given threshold minDepth. This is applied on both included and excluded counts (the latter only applies to MXE). This avoids consistency filters running on events with insufficient junction counts (leading to high variance between up/downstream values).

For an explanation of the various parameters mentioned here, see ASEFilter

Value

For runFilter and applyFilters: a vector of type logical, representing the rows of NxtSE that should be kept.

For getDefaultFilters: returns a list of default recommended filters that should be parsed into applyFilters.

Functions

• getDefaultFilters(): Returns a vector of recommended default SpliceWiz filters

• applyFilters(): Run a vector or list of ASEFilter objects on a NxtSE object

• runFilter(): Run a single filter on a NxtSE object

See Also

ASEFilter for details describing how to create and assign settings to ASEFilter objects.

Examples

# see ?makeSE on example code of how this object was generated

se <- SpliceWiz_example_NxtSE()

# Get the list of SpliceWiz recommended filters

filters <- getDefaultFilters()

# 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[applyFilters(se, getDefaultFilters()), ]

alexchwong/SpliceWiz documentation built on March 17, 2024, 3:16 a.m.