gimme_psi_mat: Extract the PSI from an inclusion table and return it as a...

In Ni-Ar/niar: Nice Interactive Analysis with R

Extract the PSI from an inclusion table and return it as a matrix

Description

The matrix contains the samples as row names and the vastID as column name

Usage

gimme_psi_mat(inclusion_tbl, vst_id, quality_thrshld = "N", verbose = FALSE)

Arguments

inclusion_tbl	path to vast-tools inclusion table that contains a vst_id event.
vst_id	vast-tools alternative splicing event to grep in the inclusion_tbl.
quality_thrshld	vast-tools event quantification quality score threshold. Must be one of "N", "VLOW", "LOW", "OK", "SOK". For more info read the official documentation here under "Column 8, score 1".
verbose	Print out extra info.

Value

A matrix

Examples

gimme_psi_mat(inclusion_tbl = /path/to/inclusion/table/file.tab,
              vst_id = "HsaEX0000001")

Ni-Ar/niar documentation built on Feb. 3, 2025, 9:25 a.m.