Read in Merscope data to an ME object

Reads in Merscope (Vizgen) molecule and boundary data from a directory, and standardises it into a MoleculeExperiment object.

Usage

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

Arguments

dataDir

Character string specifying the directory with the Cosmx output files.

keepCols

Vector of characters specifying the columns of interest from the transcripts file. "essential" selects columns with gene names, x and y locations. "all" will select all columns. Alternatively, specific colums of interest can be selected by specifying them as characters in a vector. Note that this personalised vector needs to contain the essential columns.

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, "/vizgen_HumanOvarianCancerPatient2Slice2")
meMerscope <- readMerscope(repoDir,
    keepCols = "essential",
    addBoundaries = "cell"
)
#> 
⠙ 1/2 Reading transcripts

#> 
✔ 1/2 Reading transcripts [19ms]

#> 
meMerscope
#> MoleculeExperiment class
#> 
#> molecules slot (1): detected
#> - detected:
#> samples (1): vizgen_HumanOvarianCancerPatient2Slice2
#> -- vizgen_HumanOvarianCancerPatient2Slice2:
#> ---- features (486): ACKR3 ACTA2 ... ZBED2 ZEB1
#> ---- molecules (15160)
#> ---- location range: [10219.02,10386.83] x [8350.93,8395.3]
#> 
#> 
#> boundaries slot (1): cell
#> - cell:
#> samples (1): vizgen_HumanOvarianCancerPatient2Slice2
#> -- vizgen_HumanOvarianCancerPatient2Slice2:
#> ---- segments (24): 45862 45865 ... 54562 54564