dot-categorize_diff_ase: Categorize diff ASE in to 'up' and 'down' based on log2FC,...
In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

.categorize_diff_ase

R Documentation

Categorize diff ASE in to `up` and `down` based on log2FC, p-value and p-adj values.

Description

Usually fold change 1.5 (log2FC ~0.6) and statistical significance defined by p and/or p.adj values are considered to mark gene (ASE) as differential expressed. However, these cutoffs change based on data quality. This function allows changing these cutoffs and mark genes (ASE) differently expressed. While using this package, most of the time user do not need to call this function explicitly as it is internally called by run_ase_diff_analysis().

Usage

.categorize_diff_ase(
  ase_tibble,
  log2fc_cutoff = 1,
  pval_cutoff = 0.05,
  padj_cutoff = 0.01,
  add_column_regul = TRUE,
  regul_based_upon = 1
)

Arguments

`ase_tibble`	a dataframe obtained from `SpliceWiz::ASE_*` function.
`log2fc_cutoff`, `pval_cutoff`, `padj_cutoff`	a numeric value, default `⁠(log2fc_cutoff = 1, pval_cutoff = 0.05, padj_cutoff = 0.01)⁠` denoting cutoffs. These criteria will be used to decide significance `⁠(NS, p-value, log2FC, p-value&log2FC)⁠` and type of regulation `⁠(Up, Down & other)⁠` of diff genes. See details.
`add_column_regul`	logical, default `TRUE`, indicating whether to add column `add_column_regul` or not. Added column will contain the values Up', 'Down' or 'other'.
`regul_based_upon`	one of the numeric choices 1, 2, or 3. if 1 ... Up : log2fc >= log2fc_cutoff & pvalue <= pvalue_cutoff Down : log2fc <= (-1) * log2fc_cutoff & pvalue <= pvalue_cutoff Other : remaining genes if 2 ... Up : log2fc >= log2fc_cutoff & padj <= padj_cutoff Down : log2fc <= (-1) * log2fc_cutoff & padj <= padj_cutoff Other : remaining genes if 3 ... Up : log2fc >= log2fc_cutoff & pvalue <= pvalue_cutoff & padj <= padj_cutoff Down : log2fc <= (-1) * log2fc_cutoff pvalue <= pvalue_cutoff & padj <= padj_cutoff Other : remaining genes