Quantify alternative splicing events

Quantify alternative splicing events

Usage

quantifySplicing(
  annotation,
  junctionQuant,
  eventType = c("SE", "MXE", "ALE", "AFE", "A3SS", "A5SS"),
  minReads = 10,
  genes = NULL
)

Arguments

annotation

List of data frames: annotation for each alternative splicing event type

junctionQuant

Data frame: junction quantification

eventType

Character: splicing event types to quantify

minReads

Integer: values whose number of total supporting read counts is below minReads are returned as NA

genes

Character: gene symbols for which to quantify splicing events (if NULL, events from all genes are quantified)

Value

Data frame with the quantification of the alternative splicing events

See also

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

Examples

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

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% 

#>                                  Normal 1  Normal 2  Normal 3  Cancer 1
#> SE_1_+_32_35_37_38_ACTN1        0.5000000 0.5000000 0.5000000 0.5000000
#> SE_2_+_32_35_37_38_ALDOA        0.7402597 0.5500000 0.8750000 0.6756757
#> SE_3_+_32_35_37_38_ANXA6        0.4255319 0.5121951 0.3684211 0.4418605
#> MXE_1_+_32_35_37_38_40_42_ACTN1 0.5000000 0.5000000 0.5000000 0.5000000
#> 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_1_+_32_35_37_38_ACTN1        0.5000000 0.5000000
#> SE_2_+_32_35_37_38_ALDOA        0.5744681 0.6037736
#> SE_3_+_32_35_37_38_ANXA6        0.4509804 0.4166667
#> MXE_1_+_32_35_37_38_40_42_ACTN1 0.5000000 0.5000000
#> 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