Remove alternative splicing quantification values based on coverage
Source:R/data_inclusionLevelsFilter.R
discardLowCoveragePSIvalues.Rd
Remove alternative splicing quantification values based on coverage
Usage
discardLowCoveragePSIvalues(
psi,
minReads = 10,
vasttoolsScoresToDiscard = c("VLOW", "N")
)
Arguments
- psi
Data frame or matrix: alternative splicing quantification
- minReads
Currently this argument does nothing
- vasttoolsScoresToDiscard
Character: if you are using inclusion levels from VAST-TOOLS, filter the data based on quality scores for read coverage, e.g. use
vasttoolsScoresToDiscard = c("SOK", "OK", "LOW")
to only keep events with good read coverage (by default, events are not filtered based on quality scores); read https://github.com/vastgroup/vast-tools for more information on VAST-TOOLS quality scores