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Filter alternative splicing quantification

Source: R/data_inclusionLevelsFilter.R
filterPSI.Rd

Filter alternative splicing quantification

Usage

filterPSI(
  psi,
  eventType = NULL,
  eventSubtype = NULL,
  minPSI = -Inf,
  maxPSI = Inf,
  minMedian = -Inf,
  maxMedian = Inf,
  minLogVar = -Inf,
  maxLogVar = Inf,
  minRange = -Inf,
  maxRange = Inf
)

Arguments

psi

Data frame or matrix: alternative splicing quantification

eventType

Character: filter data based on event type; check all event types available by using getSplicingEventTypes(psi), where psi is the alternative splicing quantification data; if eventType = NULL, events are not filtered by event type

eventSubtype

Character: filter data based on event subtype; check all event subtypes available in your data by using unique(getSplicingEventData(psi)$subtype), where psi is the alternative splicing quantification data; if eventSubtype = NULL, events are not filtered by event subtype

minPSI

Numeric: minimum PSI value

maxPSI

Numeric: maximum PSI value

minMedian

Numeric: minimum median PSI per splicing event

maxMedian

Numeric: maximum median PSI per splicing event

minLogVar

Numeric: minimum log10(PSI variance) per splicing event

maxLogVar

Numeric: maximum log10(PSI variance) per splicing event

minRange

Numeric: minimum PSI range across samples per splicing event

maxRange

Numeric: maximum PSI range across samples per splicing event

Value

Boolean vector indicating which splicing events pass the thresholds

See also

Other functions for PSI quantification: getSplicingEventTypes(), listSplicingAnnotations(), loadAnnotation(), plotRowStats(), quantifySplicing()

Examples

# Calculate PSI for skipped exon (SE) and mutually exclusive (MXE) events
annot <- readFile("ex_splicing_annotation.RDS")
junctionQuant <- readFile("ex_junctionQuant.RDS")

psi <- quantifySplicing(annot, junctionQuant, eventType=c("SE", "MXE"))
#> Using 3 of 3 events (100%) whose junctions are present in junction quantification data...
#>   |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 

#> Using 3 of 3 events (100%) whose junctions are present in junction quantification data...
#>   |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 

# Filter PSI
psi[filterPSI(psi, minMedian=0.05, maxMedian=0.95, minRange=0.15), ]
#>                                  Normal 1  Normal 2  Normal 3  Cancer 1
#> SE_2_+_32_35_37_38_ALDOA        0.7402597 0.5500000 0.8750000 0.6756757
#> MXE_2_+_32_35_37_38_40_42_ALDOA 0.7500000 0.6000000 0.8803828 0.6500000
#> MXE_3_+_32_35_37_38_40_42_ANXA6 0.2597403 0.4210526 0.1207729 0.3589744
#>                                  Cancer 2  Cancer 3
#> SE_2_+_32_35_37_38_ALDOA        0.5744681 0.6037736
#> MXE_2_+_32_35_37_38_40_42_ALDOA 0.5306122 0.5918367
#> MXE_3_+_32_35_37_38_40_42_ANXA6 0.4600000 0.3846154