Correct background expression in spatial transcriptomics data

This function corrects background expression in spatial transcriptomics data using specified background samples and features. It calculates background gene expression statistics and subtracts them from all samples.

Usage

CorrectBackground(
  STID_obj = NULL,
  loop_id = "LoopAllSamp",
  bg_samp_id = NULL,
  bg_features = NULL,
  PosThres_prob = 0.95,
  adjust_UMI = TRUE,
  assay_id = "Spatial",
  layer_id = "counts",
  grp_nm = NULL,
  dir_nm = "M1_CorrectBackground"
)

Arguments

STID_obj

An STID object containing spatial transcriptomics data

loop_id

Must be "LoopAllSamp" (default: "LoopAllSamp")

bg_samp_id

Character vector specifying background sample IDs

bg_features

Character vector specifying background features (genes) for correction

PosThres_prob

Numeric, probability threshold (0-1) for determining positive expression (default: 0.95)

adjust_UMI

Logical, whether to adjust correction values by mean UMI (default: TRUE)

assay_id

Character, name of the assay to use (default: "Spatial")

layer_id

Character, name of the layer/data slot to use (default: "counts")

grp_nm

Character, group name for output organization (default: NULL, uses timestamp)

dir_nm

Character, directory name for output (default: "M1_CorrectBackground")

Value

Returns the modified STID object with corrected counts in the Spatial assay

Examples

if (FALSE) { # \dontrun{
# Correct background using specified background samples and features
STID_obj <- CorrectBackground(
  STID_obj = STID_object,
  bg_samp_id = c("sample1", "sample2"),
  bg_features = c("gene1", "gene2", "gene3"),
  PosThres_prob = 0.95,
  adjust_UMI = TRUE
)
} # }