rna.read_data: Read Transcriptomics Data

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

Read Transcriptomics Data

Description

Reads transcriptomics data from one/several file(s) or dataframe and creates a SummarizedExperiment object.

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	File or dataframe containing transcriptomics data, if files.ind is not used.
files.ind	Prefixes of several files in the working directory containing transcriptomics data, if data is not used.
expdesign	Experimental design as file path or data frame, if made previously.
csvsep	Delimiter if reading CSV file(s).
dec	Decimal separator if reading CSV, TSV, or TXT files.
sheet	Sheet of an Excel file to be read.
name	Header of column containing primary gene IDs (e.g., gene names).
id	Header of column containing alternative gene IDs (e.g., locus IDs).
values	Name of the column containing the values (if files.ind != NULL).
id2name.table	File containing a table with ID to name mappings.
id2name.id	Header of column containing alternative gene IDs in id2name.table.
id2name.name	Header of column containing primary gene IDs in id2name.table.
pfx.counts	Prefix in headers of columns containing gene abundances (if data != NULL).
rsd_thresh	Provide a relative standard deviation (RSD) threshold in % for genes. The RSD is calculated for each condition and if the maximum RSD value determined for a given protein exceeds rsd_thresh, the gene is discarded. The RSD filter is applied before further missing value filters based on the three filt_ arguments.
filt_type	(Character string) "complete", "condition" or "fraction", Sets the type of filtering applied. "complete" will only keep genes with valid values in all samples. "condition" will keep genes that have a maximum of filt_thr missing values in at least one condition. "fraction" will keep genes that have a filt_min fraction of valid values in all samples.
filt_thr	(Integer) Sets the threshold for the allowed number of missing values in at least one condition if filt_type = "condition". In other words: "keep genes that have a maximum of 'filt_thr' missing values in at least one condition."
filt_min	(Numeric) Sets the threshold for the minimum fraction of valid values allowed for any genes if filt_type = "fraction".

Value

Returns a SummarizedExperiment object.

NicWir/VisomX documentation built on Dec. 8, 2024, 1:27 a.m.