rcc: Read NanoString RCC files

In TalhoukLab/nanostringr: Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data

Read NanoString RCC files

Description

Read RCC files and extract count and attribute data. Use read_rcc() for multiple files, and use the ⁠parse_*()⁠ functions for single files.

Usage

read_rcc(path = ".")

parse_counts(file)

parse_attributes(file)

Arguments

path	directory path for multiple RCC files
file	RCC file name

Details

RCC files for a sample are direct outputs from NanoString runs. We can extract counts for each gene in a sample. Sample attributes include sample ID, GeneRLF, date, cartridge ID, lane number, Fov count, Fov counted, and binding density. read_rcc() merges both count and attribute data across samples.

If path points to a zipped RCC file with multiple samples, the zip file is uncompressed and a directory of RCC sample files is created with the same name. Only file extensions ".RCC" or ".rcc" are allowed.

Value

read_rcc() reads in a directory of RCC files and outputs a list with two elements:

• raw: A tibble of parsed counts for multiple RCC files created by calling parse_counts() on each sample. Columns include "Code.Class", "Name", "Accession", and a column for each sample ID. There is one row per gene.

• exp: A tibble of parsed attributes for multiple RCC files created by calling parse_attributes() on each sample. Columns include "File.Name" (sample ID), "geneRLF", "nanostring.date", "cartridgeID", "lane.number", fov.count", "fov.counted", "binding.density". There is one row per sample.

parse_counts() reads a single RCC file and returns a tibble of parsed counts.

parse_attributes() reads a single RCC file and returns a list of parsed attributes.

Author(s)

Derek Chiu

Examples

rcc_file <- system.file("extdata", "example.RCC", package = "nanostringr")
parse_counts(rcc_file)
parse_attributes(rcc_file)

TalhoukLab/nanostringr documentation built on Aug. 24, 2023, 7:49 p.m.