Initiate an object of class SPATA2 from platform SlideSeq

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

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.