grep_psi: Grep the PSI values of an as event from a vast-tools output...

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

Grep the PSI values of an as event from a vast-tools output table.

Description

Grep the PSI values of an as event from a vast-tools output table.

Usage

grep_psi(
  inclusion_tbl,
  vst_id,
  tmp_dir = tempdir(),
  verbose = FALSE,
  clear_tmp = TRUE,
  fast_grep = TRUE,
  split_temp = TRUE
)

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
tmp_dir	path to a temporary location folder
clear_tmp	Logical, remove the temporary files after the function is done?
fast_grep	Logical, if TRUE use 'grep -m1' to stop the search after first match found. If FALSE all vst_expression_tbl is read.
split_temp	Logical, if TRUE first create a temp header file then a temp AS event file and merge them. If FALSE create one temp file with both the header and the AS event PSI and quality scores.

Value

a data.frame

Examples

#' grep_psi(path_to_vst_tbl, vst_id) |>
    tidy_vst_psi()

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