import_nanostring_rcc: Import Nanostring RCC files

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

Import Nanostring RCC files

Description

Import Nanostring RCC files

Usage

import_nanostring_rcc(
  rcc_files = NULL,
  rcc_path = ".",
  rcc_pattern = NULL,
  exclude = NULL,
  include = NULL,
  nprobes = -1,
  control_greps = c(POS = "^POS", NEG = "^NEG"),
  hk_count = 10,
  assay_name = NULL,
  curation_txt = NULL,
  return_type = c("SummarizedExperiment", "NanoString"),
  debug = FALSE,
  verbose = FALSE,
  ...
)

Arguments

rcc_files	character vector of file paths to RCC files, or if NULL then the rcc_path and rcc_pattern arguments are used to find RCC files.
rcc_path	character vector of file directories to look for RCC files, the files are matched to pattern rcc_pattern. Note the rcc_path is only used when rcc_files is not supplied.
rcc_pattern	character string containing regular expression pattern, used to match filenames which should be considered RCC files.
exclude	optional character vector of filenames to exclude from import. The filenames may be either a full file path, or the basename without the file path.
include	optional character vector of filenames to include during data import. Note that when include is defined, only these files are included in the file import, all other files are ignored.
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.
assay_name	character string of optional assay name used in the SummarizedExperiment object created. When NULL the default is "raw".
curation_txt	data.frame whose first column should match the sample column headers found in the PD abundance columns, and subsequent columns contain associated sample annotations. If curation_txt is not supplied, then values will be split into columns by ⁠_⁠ underscore or " " whitespace characters.
return_type	character string indicating the format to return. SummarizedExperiment is recommended, as the NanoString format was useful for R analysis in a package that is no longer actively maintained.
debug	logical indicating whether to send intermediate data before full processing, useful for debugging file format errors.
verbose	logical indicating whether to print verbose output.
...	additional arguments are ignored.

Details

This function reads one or more Nanostring RCC files, and produces a SummarizedExperiment object.

This function was based upon the function NanoStringNorm::read.markup.RCC(), which in our experience was problematic because it assumed all files contained identical sample annotation content.

For examples how to curate sample names into proper data.frame of experimental factors, see splicejam::curateVtoDF() or splicejam::curateDFtoDF().

Value

SummarizedExperiment or NanoString object, based upon argument return_type.

See Also

Other jam import functions: coverage_matrix2nmat(), deepTools_matrix2nmat(), frequency_matrix2nmat(), import_lipotype_csv(), import_metabolomics_niehs(), import_nanostring_csv(), 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.