Run_NxtIRF_Filters {NxtIRFcore}R Documentation

Filtering for IR and Alternative Splicing Events

Description

This function implements filtering of IR or AS events based on customisable criteria. See NxtFilter for details.

Usage

get_default_filters()

apply_filters(se, filters = get_default_filters())

runFilter(se, filterObj)

Arguments

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.

Details

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

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

Value

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.

Functions

See Also

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

Examples

# 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()), ]

[Package NxtIRFcore version 0.99.11 Index]