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.