getTechTxFields: Get relevant fields and file paths for transcript spots

View source: R/utils.R

getTechTxFieldsR Documentation

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 Dec. 20, 2024, 3:41 a.m.