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Filenames.R
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Filenames.R
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# Filenames that are used in multiple files
dir_data <- "data"
dir_figures <- "figures"
dir_input <- file.path(dir_data, "input")
dir_pseudobulk <- file.path(dir_data, "pseudobulk")
dir_output <- file.path(dir_data, "output")
dir_metadata <- file.path(dir_data, "metadata")
dir_tmp <- file.path(dir_data, "tmp")
dir_markers <- file.path(dir_data, "markers")
dir_signatures <- file.path(dir_data, "signatures")
dir_cibersort_corrected_signatures <- file.path(dir_signatures, "cibersortx_batch_corrected")
dir_cibersort <- "/data" # outside this working directory, gets shared with cibersort docker
dir_estimates <- file.path(dir_output, "estimates")
dir_top_estimates <- file.path(dir_output, "top_estimates")
dir_errors <- file.path(dir_output, "errors")
dir_top_parameters <- file.path(dir_output, "top_parameters")
dir_best_errors <- file.path(dir_output, "best_errors")
dir_estimates_tmp <- file.path(dir_estimates, "tmp")
dir_errors_tmp <- file.path(dir_errors, "tmp")
dir_scaden_models <- file.path(dir_output, "scaden_models")
dir_music_basis <- file.path(dir_output, "music_basis")
dir_hspe_params <- file.path(dir_output, "hspe_params")
dir_raw_data <- file.path(dir_input, "raw_data")
dir_preprocessed <- file.path(dir_input, "preprocessed")
dir_map_reference <- file.path(dir_input, "map_reference")
dir_covariates <- file.path(dir_metadata, "covariates")
dir_cain_raw <- file.path(dir_raw_data, "cain_raw")
dir_lau_raw <- file.path(dir_raw_data, "lau_raw")
dir_leng_raw <- file.path(dir_raw_data, "leng_raw")
dir_mathys_raw <- file.path(dir_raw_data, "mathys_raw")
dir_morabito_raw <- file.path(dir_raw_data, "morabito_raw")
dir_seaad_raw <- file.path(dir_raw_data, "sea-ad_raw")
dir_mayo_raw <- file.path(dir_raw_data, "mayo_raw")
dir_msbb_raw <- file.path(dir_raw_data, "msbb_raw")
dir_rosmap_raw <- file.path(dir_raw_data, "rosmap_raw")
file_searef_h5 <- file.path(dir_seaad_raw, "ref_counts.h5ad")
file_seaad_h5 <- file.path(dir_seaad_raw, "seaad_counts.h5ad")
url_searef_h5 <- "https://sea-ad-single-cell-profiling.s3.amazonaws.com/MTG/RNAseq/Reference_MTG_RNAseq_final-nuclei.2022-06-07.h5ad"
url_seaad_h5 <- "https://sea-ad-single-cell-profiling.s3.amazonaws.com/MTG/RNAseq/SEAAD_MTG_RNAseq_final-nuclei.2023-05-05.h5ad"
url_seaad_merfish <- "https://sea-ad-single-cell-profiling.s3.amazonaws.com/MTG/MERFISH/SEAAD_MTG_MERFISH_all-nuclei.2023-05-08.h5ad"
dir_mayo_output <- file.path(dir_estimates, "Mayo")
dir_msbb_output <- file.path(dir_estimates, "MSBB")
dir_rosmap_output <- file.path(dir_estimates, "ROSMAP")
file_gene_list <- file.path(dir_metadata, "ensembl_gene_list.csv")
file_rosmap_ihc_proportions <- file.path(dir_metadata, "ihc_proportions_normalized.csv")
# Make sure these directories exist
for (D in ls(pattern = "dir_")) {
dir.create(eval(parse(text = D)), recursive = TRUE, showWarnings = FALSE)
}