run_ase_diff_analysis: Perform ASE diff analysis using edgeR.

In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

Perform ASE diff analysis using edgeR.

Description

Perform ASE diff analysis using edgeR.

Usage

run_ase_diff_analysis(
  x,
  test_nom,
  test_denom,
  test_factor = "condition",
  cutoff_lfc = 1,
  cutoff_pval = 0.05,
  cutoff_padj = 0.01,
  regul_based_upon = 1,
  n_thread = 1,
  ...
)

Arguments

x	an object of class NxtSe.
test_nom	// TO DO
test_denom	// TO DO
test_factor	refer to the argument test_factor in SpliceWiz::ASE_edgeR().
cutoff_lfc	minimal threshold for log2fold change, default 1 (2 fold).
cutoff_pval	minimal threshold for pvalue, default 0.05. P-value threshold will be applied only when regul_based_upon is either 1 or 3.
cutoff_padj	minimal threshold for Padj, default 0.01. Padj threshold will be applied only when regul_based_upon is either 2 or 3.
regul_based_upon	one of the numeric choices 1, 2, or 3. Default 1 i.e. categorized diff. ASE by pvalue and log2fc. if 1 ... Up : log2fc >= cutoff_lfc & pvalue <= cutoff_pval Down : log2fc <= (-1) * cutoff_lfc & pvalue <= cutoff_pval Other : remaining genes if 2 ... Up : log2fc >= cutoff_lfc & padj <= cutoff_padj Down : log2fc <= (-1) * cutoff_lfc & padj <= cutoff_padj Other : remaining genes if 3 ... Up : log2fc >= cutoff_lfc & pvalue <= cutoff_pval & padj <= cutoff_padj Down : log2fc <= (-1) * cutoff_lfc & pvalue <= cutoff_pval & padj <= cutoff_padj Other : remaining genes
n_thread	an integer, default 1, denoting number of threads to use for multitasking.
...	Other parameters passed to SpliceWiz::ASE_edgeR().

Value

an object of class parcutils_se.

Examples

se <- SpliceWiz::SpliceWiz_example_NxtSE(novelSplicing = TRUE)
SpliceWiz::colData(se)$treatment <- rep(c("A", "B"), each = 3)
SpliceWiz::colData(se)$replicate <- rep(c("P","Q","R"), 2)
run_ase_diff_analysis(x = se, test_factor = "treatment", test_nom = "A" ,test_denom = "B",  IRmode ="annotated")
run_ase_diff_analysis(x = se, test_factor = "treatment", test_nom = "A" ,test_denom = "B",  IRmode ="annotated",  cutoff_lfc = 0.6, cutoff_padj = 1, regul_based_upon = 2, n_thread = 2  )

cparsania/parcutils documentation built on Oct. 27, 2024, 4:55 a.m.