Read in Cosmx data (Nanostring) as an ME object.

This function is a wrapper around the readMolecules function. It can read both molecule and mask information. The segmentation masks are converted to boundaries, and these are added to the boundaries slot of the MoleculeExperiment object.

Usage

readCosmx(dataDir, keepCols = "essential", addBoundaries = "cell")

Arguments

dataDir

Character string specifying the directory with the Cosmx output files.

keepCols

Character string specifying which columns to keep. Defaults to "essential". The other option is to select "all", or custom columns by specifying their names in a vector.

addBoundaries

A string with which to specify the name of the boundary assay to be added to the me object. Can be a string, or NULL. If NULL, a simple ME object with no boundaries will be created.

Value

A MoleculeExperiment object

Examples

repoDir <- system.file("extdata", package = "MoleculeExperiment")
repoDir <- paste0(repoDir, "/nanostring_Lung9_Rep1")
#
meCosmx <- readCosmx(repoDir,
    keepCols = "essential"
)
#> 
⠙ 1/3 Reading transcripts

#> 
✔ 1/3 Reading transcripts [45ms]

#> 
#> 
⠙ 2/3 Transforming masks into polygons

#> 
✔ 2/3 Transforming masks into polygons [66ms]

#> 
#> 
⠙ 3/3 Merging patches

#> 
✔ 3/3 Merging patches [35ms]

#> 
meCosmx
#> MoleculeExperiment class
#> 
#> molecules slot (1): detected
#> - detected:
#> samples (2): sample_1 sample_2
#> -- sample_1:
#> ---- features (969): AATK ABL1 ... YES1 ZFP36
#> ---- molecules (23844)
#> ---- location range: [924.01,1031.94] x [26290,26398]
#> -- sample_2:
#> ---- features (943): AATK ABL1 ... YBX3 ZFP36
#> ---- molecules (7155)
#> ---- location range: [2894.03,3002] x [26290.05,26398]
#> 
#> 
#> boundaries slot (1): cell
#> - cell:
#> samples (2): sample_1 sample_2
#> -- sample_1:
#> ---- segments (113): 1 2 ... 112 113
#> -- sample_2:
#> ---- segments (83): 114 115 ... 195 196