NxtFilter-class {NxtIRFcore}R Documentation

NxtIRF filters to remove low-abundance alternative splicing and intron retention events

Description

NxtIRF filters to remove low-abundance alternative splicing and intron retention events

Usage

NxtFilter(
  filterClass = c("Data", "Annotation"),
  filterType = c("Depth", "Coverage", "Consistency", "Protein_Coding", "NMD", "TSL"),
  pcTRUE = 100,
  minimum = 20,
  maximum = 1,
  minDepth = 5,
  condition = "",
  minCond = -1,
  EventTypes = c("IR", "MXE", "SE", "A3SS", "A5SS", "AFE", "ALE", "RI")
)

Arguments

filterClass

Must be either "Data" or "Annotation". See details

filterType

If filterClass = "Data", then must be one of c("Depth", "Coverage", "Consistency"). If filterClass = "Annotation", must be one of c("Protein_Coding", "NMD", "TSL"). See details

pcTRUE

If conditions are set, what percentage of all samples in each of the condition must the filter be satisfied for the event to pass the filter check. Must be between 0 and 100 (default 100)

minimum

Filter-dependent argument. See details

maximum

Filter-dependent argument. See details

minDepth

Filter-dependent argument. See details

condition

(default "") If set, must match the name of an experimental condition in the NxtSE object to be filtered, i.e. a column name in colData(se). Leave blank to disable filtering by condition

minCond

(default -1) If condition is set, how many minimum number of conditions must pass the filter criteria. For example, if condition = "Batch", and batches are "A", "B", or "C", setting minCond = 2 with pcTRUE = 100 means that all samples belonging to two of the three types of Batch must pass the filter criteria. Setting -1 means all elements of condition must pass criteria. Set to -1 when the number of elements in the experimental condition is unknown. Ignored if condition is left blank.

EventTypes

What types of events are considered for filtering. Must be one of c("IR", "MXE", "SE", "A3SS", "A5SS", "AFE", "ALE", "RI"). Events not specified in EventTypes are not filtered (i.e. they will pass the filter without checks)

Details

Annotation Filters

We highly recommend using the default filters, which can be acquired using get_default_filters

Value

A NxtFilter object with the specified parameters

Functions

See Also

Run_NxtIRF_Filters

Examples

# Create a NxtFilter that filters for protein-coding ASE
f1 <- NxtFilter(filterClass = "Annotation", filterType = "Protein_Coding")

# Create a NxtFilter that filters for Depth >= 20 in IR events
f2 <- NxtFilter(
    filterClass = "Data", filterType = "Depth",
    minimum = 20, EventTypes = c("IR", "RI")
)

# Create a NxtFilter that filters for Coverage > 60% in splice events
# that must be satisfied in at least 2 categories of condition "Genotype"
f3 <- NxtFilter(
    filterClass = "Data", filterType = "Coverage",
    minimum = 60, EventTypes = c("MXE", "SE", "AFE", "ALE", "A3SS", "A5SS"),
    condition = "Genotype", minCond = 2
)

# Create a NxtFilter that filters for Depth > 10 in all events
# that must be satisfied in at least 50% of each gender
f4 <- NxtFilter(
    filterClass = "Data", filterType = "Depth",
    minimum = 10, condition = "gender", pcTRUE = 50
)

# Get a description of what these filters do:
f1
f2
f3
f4


[Package NxtIRFcore version 0.99.11 Index]