initiateSpataObjectSlideSeqV1: Initiate an object of class 'SPATA2' from platform SlideSeq

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Initiate an object of class SPATA2 from platform SlideSeq

Description

Wrapper function around the necessary content to create a SPATA2 object from the standardized output of the SlideSeqV1 platform.

Usage

initiateSpataObjectSlideSeqV1(
  sample_name,
  directory_slide_seq,
  file_counts = NULL,
  file_barcodes = NULL,
  file_genes = NULL,
  file_coords = NULL,
  verbose = TRUE
)

Arguments

sample_name	Character value. The name with which to identify the SPATA2 object.
directory_slide_seq	Character value. Directory to a SlideSeq folder that contains a count matrix and bead locations.
file_counts	Character value or NULL. If character, specifies the filename of the count matrix. If NULL, the SlideSeq folder is skimmed for a file ending with .mtx.
file_barcodes	Character value or NULL. If character, specifies the filename of the barcode names for the count matrix if it does not contain column names. If NULL, the SlideSeq folder is skimmed for a file ending with barcodes.tsv.
file_genes	Character value or NULL. If character, specifies the filename of the gene names for the count matrix if it does not contain row names. If NULL, the SlideSeq folder is skimmed for a file ending with genes.tsv.
file_coords	Character value or NULL. If character, specifies the filename of the coordinates. If NULL, the SlideSeq folder is skimmed for a file ending with MatchedBeadLocation.csv.
verbose	Logical. If TRUE, informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Value

An object of class SPATA2.

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.