inDAGO (version 1.0.0)

GetEdgerY: 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
)

Value

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

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")