GetEdgerY: GetEdgerY

In inDAGO: A GUI for Dual and Bulk RNA-Sequencing Analysis

GetEdgerY

Description

Calculate and return filtered DGEList object and log-CPM matrices using edgeR and optional HTSFilter

Usage

GetEdgerY(
  gr,
  WDpn,
  colIDgene,
  colCounts,
  skip_preN,
  filterMethod,
  min_count,
  min_total_count,
  large_n,
  min_prop,
  normMethod
)

Arguments

gr	Data frame with sample metadata, including sample names and group labels
WDpn	Directory containing count files (*.tab)
colIDgene	Column index of gene IDs in count files
colCounts	Column index of counts in count files
skip_preN	Number of header lines to skip in count files
filterMethod	Either "filterByExpr" or "HTSFilter"
min_count	Minimum count per gene (filterByExpr)
min_total_count	Minimum total count per gene (filterByExpr)
large_n	Number of samples per group to consider as "large" (filterByExpr)
min_prop	Minimum proportion of samples with expression (filterByExpr)
normMethod	Normalization method (e.g., "TMM", "RLE")

Value

A list with total/kept gene counts, filtered DGEList objects, and log-CPM matrices

inDAGO documentation built on Aug. 8, 2025, 7:47 p.m.