Read NanoString RCC files

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

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.

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.

Author

Derek Chiu

Examples

rcc_file <- system.file("extdata", "example.RCC", package = "nanostringr")
parse_counts(rcc_file)
#> # A tibble: 354 × 4
#>    Code.Class Name    Accession      `TAOC00241-N1`
#>    <chr>      <chr>   <chr>                   <int>
#>  1 Endogenous COL1A1  NM_000088.3             47179
#>  2 Endogenous ADAM12  NM_003474.4               158
#>  3 Endogenous BRCA2   NM_000059.3                32
#>  4 Endogenous GTF2H5  NM_207118.2               117
#>  5 Endogenous SLC7A11 NM_014331.3                33
#>  6 Endogenous HIF1A   NM_001530.2               691
#>  7 Endogenous DCN     NM_001920.3              2431
#>  8 Endogenous SVIL    NM_003174.2               335
#>  9 Endogenous HBB     NM_000518.4               292
#> 10 Endogenous MRPS27  NM_001286748.1             91
#> # ℹ 344 more rows
parse_attributes(rcc_file)
#> $File.Name
#> [1] "TAOC00241-N1"
#> 
#> $geneRLF
#> [1] "OTTA2017_C6082"
#> 
#> $nanostring.date
#> [1] "2018-07-24"
#> 
#> $cartridgeID
#> [1] "OTTA2-108-SYD-20H"
#> 
#> $lane.number
#> [1] "4"
#> 
#> $fov.count
#> [1] 555
#> 
#> $fov.counted
#> [1] 542
#> 
#> $binding.density
#> [1] 0.27
#>