Read RCC files and extract count and attribute data. Use
multiple files, and use the
parse_*() functions for single files.
read_rcc(path = ".") parse_counts(file) parse_attributes(file)
directory path for multiple RCC files
RCC file name
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
read_rcc() merges both count and attribute data across
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.
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
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
parse_attributes() reads a single RCC file and returns a list of
rcc_file <- system.file("extdata", "example.RCC", package = "nanostringr") parse_counts(rcc_file) parse_attributes(rcc_file)
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