This function runs the TMAtools pipeline for multiple TMA directories. It combines TMA datasets, deconvolutes the combined dataset, and translates numerical biomarker scores to nominal scores.
Usage
tmatools(
tma_dirs,
biomarker_rules_file,
output_dir = "tmatools_output",
combined_tma_file = "1_combined_tma.xlsx",
deconvoluted_tma_file = "2_deconvoluted_tma.xlsx",
translated_tma_file = "3_translated_tma.xlsx",
consolidated_tma_file = "4_consolidated_tma.xlsx",
final_tma_file = "5_final_consolidated_tmas.xlsx",
biomarker_sheet_index = 2
)Arguments
- tma_dirs
A character vector of TMA directory paths.
- output_dir
The directory where the output files will be saved.
- combined_tma_file
The name of the combined TMA file.
- deconvoluted_tma_file
The name of the deconvoluted TMA file.
- consolidated_tma_file
The name of the consolidated TMA file.
- final_tma_file
The name of the final file containing the consolidated scores from multiple TMAs processed.
- biomarker_sheet_index
The index of the biomarker sheet in the TMA file.
Examples
library(TMAtools)
tma_dirs <- c(
system.file("extdata", "tma1", package = "TMAtools"),
system.file("extdata", "tma2", package = "TMAtools")
)
# Run the TMAtools pipeline
tmatools(
tma_dirs = tma_dirs,
output_dir = "tmatools_output"
)
#> Error in tmatools(tma_dirs = tma_dirs, output_dir = "tmatools_output"): argument "biomarker_rules_file" is missing, with no default