Created
November 1, 2023 21:50
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| library(IDBacApp) | |
| library(dplyr) | |
| library(DBI) | |
| library(pool) | |
| library(coop) | |
| # Change this to be the full file path to your sqlite file | |
| sqlite_filepath <- "/home/chase/Downloads/NK_Library_Full_Up_To_2023-10-02-Copy.sqlite" | |
| db_pool <- IDBacApp::idbac_connect(fileName = tools::file_path_sans_ext(basename(sqlite_filepath)), | |
| filePath = dirname(sqlite_filepath))[[1]] | |
| # Update the database to the latest version | |
| idbac_update_db(pool = db_pool, copy_overwrite = "overwrite") | |
| # Reconnect to the database | |
| db_pool <- IDBacApp::idbac_connect(fileName = tools::file_path_sans_ext(basename(sqlite_filepath)), | |
| filePath = dirname(sqlite_filepath))[[1]] | |
| # Peak at the tables in the SQLite database | |
| sapply(DBI::dbListTables(conn = db_pool), | |
| function(x){ | |
| print(dplyr::tbl(db_pool, x ) %>% head()) | |
| }, simplify = F) | |
| tbl(db_pool, "spectra") %>% filter(max_mass > 6000) %>% pull("strain_id") %>% unique -> sample_ids | |
| # Enter your sample IDs here or comment/delete and then it will compare all samles in the DB using the sample_ids from the line above | |
| #sample_ids <- c("A1", "MHB") | |
| # Adjust the variables for mass cutoffs etc, below | |
| temp <- lapply(sample_ids, | |
| function(ids){ | |
| IDBacApp::idbac_get_peaks(pool = db_pool, | |
| sampleIDs = ids, | |
| minFrequency = 0, | |
| minNumber = NA, | |
| lowerMassCutoff=3000, | |
| upperMassCutoff = 15000, | |
| minSNR = 3, | |
| tolerance = 0.002, | |
| type = "protein", | |
| mergeReplicates = TRUE)[[1]] | |
| }) | |
| names(temp) <- c(sample_ids) | |
| # Adjust the variables for mass cutoffs etc, below. It's complicated but ppm isn't a direct cutoff, it controls how the peaks are "fuzzified" | |
| fuzzy_vec <- IDBacApp::createFuzzyVector( | |
| massStart =3000, | |
| massEnd = 15000, | |
| ppm = 1000, | |
| massList = lapply(temp, function(x) x@mass), | |
| intensityList = lapply(temp, function(x) x@intensity) | |
| ) | |
| # Print distance matrix between samples | |
| write.csv(round(as.data.frame((1 - coop::cosine(fuzzy_vec))), 2), "results.csv") |
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Created on 2023-11-01 with reprex v2.0.2
Session info