ReadDataFCS: Read in FCS file

In CamaraLab/STvEA: Spatially-resolved Transcriptomics via Epitope Anchoring

Read in FCS file

Description

Read in FCS file

Usage

ReadDataFCS(
  path_to_fcs,
  is_protein,
  is_blank,
  protein_names = NULL,
  tile_relative = FALSE,
  num_tile_x = 9,
  x_pix_size = 188,
  y_pix_size = 188,
  z_pix_size = 900,
  stvea_object = NULL
)

Arguments

path_to_fcs	readable path to FCS file
is_protein	boolean vector indicating which columns in FCS should be kept as protein expression for downstream analyses
is_blank	boolean vector indicating which columns in FCS are blank for filtering purposes
protein_names	vector of names for each protein channel column - if null, will keep column names from FCS
tile_relative	whether x,y,z coordinates are relative to x_tile,y_tile (TRUE) or to corner of image (FALSE). If TRUE, will compute absolute coordinates If FALSE, will just take given x,y,z coordinates
num_tile_x	number of tiles in the x direction, only used if tile_relative = TRUE and the tile information in the FCS file is saved as tile_nr instead of x_tile,y_tile
x_pix_size	x dimension of pixel coordinates in nm. Set to 1 to keep pixel dimensions.
y_pix_size	y dimension of pixel coordinates in nm. Set to 1 to keep pixel dimensions.
z_pix_size	z dimension of pixel coordinates in nm. Set to 1 to keep pixel dimensions.
stvea_object	(optional) Pre-existing STvEA.data object to load data into. If not provided, a new object is created.

Value

STvEA.data class object

CamaraLab/STvEA documentation built on April 2, 2024, 6:07 a.m.