getTechTxFields: Get relevant fields and file paths for transcript spots

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

Get relevant fields and file paths for transcript spots

Description

Get column names for x, y, and z coordinates, gene IDs, and cell IDs from the transcript file and get file paths for transcript spot coordinates given technology.

Usage

getTechTxFields(tech, data_dir = NULL)

Arguments

tech	Name of the commercial technology, must be one of Vizgen, Xenium, and CosMX.
data_dir	Top level directory of the output.

Value

A named list with elements:

spatialCoordsNames

A character vector for column names for the xyz coordinates of the transcript spots.

gene_col

Column name for gene IDs.

cell_col

Column name for cell IDs.

fn

File path of the transcript spot file.

pachterlab/SpatialFeatureExperiment documentation built on Jan. 29, 2025, 10:32 p.m.