Remove alternative splicing quantification values based on coverage

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

Value

Alternative splicing quantification data with missing values for any values with insufficient coverage