import_nanostring_csv: Import Nanostring csv file

In jmw86069/platjam: Platform Jam, biological platform importers.

Import Nanostring csv file

Description

Import Nanostring csv file

Usage

import_nanostring_csv(
  csv,
  probe_colname = "Probe_ID",
  probe_anno_file = NULL,
  assay_name = NULL,
  hk_count = 10,
  curation_txt = NULL,
  verbose = FALSE,
  ...
)

Arguments

csv	character path to CSV file, suitable for import by data.table::fread(), so most delimiters will be recognized.
probe_colname	character string used to define the probe identifier in rowData(), derived from the colnames() of the import data. Sometimes the values represent "Probe_ID", and sometimes they may represent "Gene", "miRNA" or another measurement.
probe_anno_file	character path to one or more files with additional annotation for each measurement, with identifiers that match probe_colname above.
assay_name	character string of optional assay name used in the SummarizedExperiment object created. When NULL the default is "raw" unless the file contains substring "norm" in which case it uses "norm".
hk_count	integer number of housekeeper genes to use when "control_type" is not defined for the imported data. In this case, the last hk_count genes in the data are assumed to be housekeeper genes, by typical convention of NanoString codeset design.
curation_txt	either data.frame or character file path to tab- or comma-delimited file. The first column should match the column headers after importing data, colData(se). Subsequent columns contain associated sample annotations. For Nanostring data, the Nanostring sample annotations will already be associated with the colData(se), and colnames(curation_df) will overwrite any that already exist. Pro tip: The first column in curation_txt should contain '.' instead of punctuation/whitespace, to improve pattern matching filenames where the punctuation characters may have been modified during processing. Note also that when curation_txt is supplied, samples in se will be subset to include only those samples that match curation_txt, and in the order they appear in the curation_txt file. This behavior allows the curation_txt to be used to define the appropriate experimental ordering, which by default also defines downstream control factor levels for statistical contrasts. The first factor level is used as the control value in those contrasts.
verbose	logical indicating whether to print verbose output.
...	additional arguments are ignored.

Value

SummarizedExperiment

See Also

Other jam import functions: coverage_matrix2nmat(), deepTools_matrix2nmat(), frequency_matrix2nmat(), import_lipotype_csv(), import_metabolomics_niehs(), import_nanostring_rcc(), import_nanostring_rlf(), import_omics_data(), import_proteomics_PD(), import_proteomics_mascot(), import_salmon_quant(), process_metab_compounds_file()

jmw86069/platjam documentation built on Sept. 26, 2024, 3:31 p.m.