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
A path to a single TMA directory, which must contain:
Score sheets: one or more Excel files with biomarker scores (one biomarker per sheet).Clean map: an Excel file with "clean_map" in the file name. This file corresponds to the sector map of your TMA that only contains the core IDs within the corresponding cells. No other annotation outside the map is allowed, asTMAtoolsuses the exact positions of core IDs to map corresponding scores. Optional:Metadata: An Excel file with "metadata" in the name. In a single tab, it must contain at least two columns: "core_id" (core IDs that appear in the sector map) and "accession_id" (case or patient identifiers). Optionally, you can add other columns with additional metadata (e.g., age, sex, histotype, block number), which will be carried forward to your output files.
- 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 with combined biomarker data (scores + map). Each item of the list will be one sheet in the output Excel file.
Examples
library(TMAtools)
# grab folder with example TMA datasets
tma_dir <- system.file("extdata", "tma1", package = "TMAtools")
# define output files
combined_tma_file <- "combined_tma.xlsx"
# combine TMA datasets
combined_data_list <- combine_tma_spreadsheets(
tma_dir = tma_dir,
output_file = combined_tma_file,
biomarker_sheet_index = 2,
valid_biomarkers = c("ER", "p53") # optional, but recommended to avoid misspelling errors
)
print(combined_data_list)
#> $`TMA map`
#> # A tibble: 9 × 13
#> `` `` `` `` `` `` `` `` `` `` `` `` ``
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 2 NA NA 1 1 1 2 2 NA 6 6 6 7 7
#> 3 NA NA 4 3 3 3 2 NA 9 8 8 8 7
#> 4 NA NA 4 4 5 5 5 NA 9 9 NA NA NA
#> 5 NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 6 NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 7 NA NA 10 10 10 11 11 NA 15 15 15 16 16
#> 8 NA NA 13 12 12 12 11 NA NA NA 17 17 17
#> 9 NA NA 13 13 14 14 14 NA NA NA NA NA NA
#>
#> $ER
#> # A tibble: 9 × 13
#> `` `` `` `` `` `` `` `` `` `` `` `` ``
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 2 NA NA 9 9 9 1 2 NA x 2 2 x 1
#> 3 NA NA 2 2 x 1 2 NA 0 0 1 x x
#> 4 NA NA 0 0 2 2 2 NA 1 x NA NA NA
#> 5 NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 6 NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 7 NA NA x 9 0 2 x NA 1 1 2 x 2
#> 8 NA NA 9 9 x 9 0 NA NA NA 0 1 2
#> 9 NA NA 1 1 1 2 1 NA NA NA NA NA NA
#>
#> $p53
#> # A tibble: 9 × 13
#> `` `` `` `` `` `` `` `` `` `` `` `` ``
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 2 NA NA 3 0 5 8 9 NA 5 3 3 4 4
#> 3 NA NA 8 5 9 9 x NA 3 x 9 3 5
#> 4 NA NA 4 4 3 2 1 NA 3 2 NA NA NA
#> 5 NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 6 NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 7 NA NA 3 5 5 8 9 NA 3 x 1 8 4
#> 8 NA NA 5 1 2 4 5 NA NA NA 8 3 2
#> 9 NA NA 1 3 3 4 5 NA NA NA NA NA NA
#>