View source: R/Script_PLATE_03_COMPUTE_PSI_0_Compute.R
ComputePSI | R Documentation |
Validate splicing events and subsequently computes percent spliced-in (PSI) values these high-quality splicing events. This is a wrapper function for ComputePSI.SE
, ComputePSI.MXE
, ComputePSI.A5SS
, ComputePSI.A3SS
, ComputePSI.RI
, ComputePSI.AFE
, and ComputePSI.ALE
functions.
ComputePSI( MarvelObject, CoverageThreshold, EventType, thread = NULL, UnevenCoverageMultiplier = 10, read.length = 1 )
MarvelObject |
Marvel object. S3 object generated from |
CoverageThreshold |
Numeric value. Coverage threshold below which the PSI of the splicing event will be censored, i.e. annotated as missing (NA). Coverage defined as the total number of reads supporting both included and excluded isoforms. |
EventType |
Character string. Indicate which splicing event type to calculate the PSI values for. Can take value |
thread |
Numeric value. Only applicable when |
UnevenCoverageMultiplier |
Numeric value. Maximum allowable fold difference between two included junction counts for SE or two included or two excluded junction counts for MXE. Only applicable when |
read.length |
Numeric value. The length of read.Only applicable when |
An object of class S3 with new slots $SpliceFeatureValidated
and $PSI
.
marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL")) marvel.demo <- ComputePSI(MarvelObject=marvel.demo, CoverageThreshold=10, EventType="SE", UnevenCoverageMultiplier=10 )
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