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Combine TMA spreadsheets

Source: R/combine_tma_spreadsheets.R
combine_tma_spreadsheets.Rd

This function combines multiple TMA spreadsheets into a single spreadsheet that can be used for deconvolution with TMAtools::deconvolute().

Usage

combine_tma_spreadsheets(
  tma_dir,
  output_file = "combined_tma_spreadsheet.xlsx",
  biomarker_sheet_index = 2,
  valid_biomarkers = NULL,
  tma_name = NULL
)

Arguments

tma_dir

The directory containing the TMA spreadsheets. This directory must contain:

  • One or more excel files for the scores of some biomarker (s)

  • One excel file with "metadata" in the file name

  • One excel file with "clean_tma" in the file name

output_file

The name of the output file.

biomarker_sheet_index

The index of the sheet used for ALL files for the biomarker scores.

valid_biomarkers

Optional character vector of biomarkers to check against.

tma_name

name of TMA used in error message only.

Value

List of data frames (invisible).

Examples

library(TMAtools)
tma_dir <- system.file("extdata", package = "TMAtools")
combine_tma_spreadsheets(
    tma_dir = tma_dir,
    output_file = "combined_tma_spreadsheet.xlsx",
    biomarker_sheet_index = 2
)
#> Error in combine_tma_spreadsheets(tma_dir = tma_dir, output_file = "combined_tma_spreadsheet.xlsx",     biomarker_sheet_index = 2): FATAL - missing TMA clean map
# check the output Excel file, which should then be used as
# the input for `TMAtools::deconvolute()`