convert_psi: Convert low/bad quality PSI values to NA

In kcha/psiplot: Generate plots of PSI values generated by vast-tools

Convert low/bad quality PSI values to NA

Description

Helper function to filter and return PSI values. PSIs are converted to NA if first coverage code is 'N' e.g. PSI=100, Coverage=N,N,N,OK,S —> PSI=NA For internal use. Called by format_table.

Usage

convert_psi(t, qual = c("VLOW", "N", "LOW", "OK", "SOK"))

Arguments

t	Original PSI plus quality scores data frame WITHOUT the exon metadata columns
qual	String indicating the minimun vast-tools quality score for the PSI to be accepted. Defaults to 'VLOW'. See the vast-tools documentation for details.

Value

Data frame with the same dimensions as t and low/bad quality P SI values converted to NA

Examples

## Not run: 
psiplot:::convert_psi(psi[,7:ncol(psi)])

## End(Not run)

kcha/psiplot documentation built on March 27, 2022, 4:20 a.m.