rna.read_data: Read transcriptomics data

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

Read transcriptomics data

Description

Imports count tables (CSV/TSV/XLS/XLSX) or data frames and returns a SummarizedExperiment, with optional RSD and missing-value filtering.

Usage

rna.read_data(
  data = NULL,
  files.ind = NULL,
  expdesign = NULL,
  csvsep = ";",
  dec = ".",
  sheet = 1,
  name = "SymbolID",
  id = "gene_id",
  values = "FPKM",
  id2name.table = NULL,
  id2name.id = NULL,
  id2name.name = NULL,
  pfx.counts = "counts.",
  rsd_thresh = NULL,
  filt_type = c("condition", "complete", "fraction", NULL),
  filt_thr = 3,
  filt_min = NULL
)

Arguments

data	Data frame or file path for a count table.
files.ind	Character; prefix for matching multiple files in the working directory.
expdesign	Experimental design as data frame or file path.
csvsep	Field separator for CSV files (default ";").
dec	Decimal separator for CSV/TSV/TXT files (default ".").
sheet	Sheet number or name for Excel files.
name	Column name for primary gene IDs.
id	Column name for alternative gene IDs.
values	Column name for count values when using files.ind.
id2name.table	Optional ID→name mapping table or file path.
id2name.id	Column name of alternative IDs in mapping table.
id2name.name	Column name of primary IDs in mapping table.
pfx.counts	Prefix for abundance column names.
rsd_thresh	Numeric; RSD threshold (%) for filtering genes.
filt_type	Character; one of "complete", "condition", or "fraction" for missing-value filtering.
filt_thr	Numeric; threshold for missing-value count per condition.
filt_min	Numeric; minimum fraction of valid values required.

Value

A SummarizedExperiment object with filtered and processed counts.

NicWir/VisomX documentation built on July 17, 2025, 12:08 a.m.