| |
| |
| |
| library(GEOquery) |
| library(limma) |
| library(hgu219.db) |
| library(umap) |
| library(here) |
| library(tidyverse) |
|
|
| |
|
|
| dir.create("data/gse65682") |
| gset <- getGEO("GSE65682", destdir = "data/gse65682", GSEMatrix = TRUE, getGPL = FALSE) |
| if (length(gset) > 1) idx <- grep("GPL13667", attr(gset, "names")) else idx <- 1 |
| gset <- gset[[idx]] |
|
|
| ex <- exprs(gset) |
| |
| qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm = T)) |
| LogC <- (qx[5] > 100) || |
| (qx[6] - qx[1] > 50 && qx[2] > 0) |
| if (LogC) { |
| ex[which(ex <= 0)] <- NaN |
| ex <- log2(ex) |
| } |
|
|
| |
| dev.new(width = 3 + ncol(gset) / 6, height = 5) |
| par(mar = c(7, 4, 2, 1)) |
| title <- paste("GSE65682", "/", annotation(gset), sep = "") |
| boxplot(ex, boxwex = 0.7, notch = T, main = title, outline = FALSE, las = 2) |
| dev.off() |
|
|
| |
| par(mar = c(4, 4, 2, 1)) |
| title <- paste("GSE65682", "/", annotation(gset), " value distribution", sep = "") |
| plotDensities(ex, main = title, legend = F) |
|
|
| |
| ex <- na.omit(ex) |
| plotSA(lmFit(ex), main = "Mean variance trend, GSE65682") |
|
|
| |
| ex <- ex[!duplicated(ex), ] |
| ump <- umap(t(ex), n_neighbors = 15, random_state = 123) |
| plot(ump$layout, main = "UMAP plot, nbrs=15", xlab = "", ylab = "", pch = 20, cex = 1.5) |
|
|
| clean_char <- function(x, prefix_regex) { |
| val <- str_squish(str_remove(x, prefix_regex)) |
| na_if(val, "NA") |
| } |
|
|
| pdat_mars <- as_tibble(pData(gset), rownames = "sample_id") |> |
| select(sample_id, starts_with("characteristics")) |
|
|
| purrr::imap(pdat_mars |> select(-sample_id), ~ count(tibble(value = .x), value, name = "n") |> arrange(desc(n))) |
|
|
| gse65682_metadata <- as_tibble(pData(gset), rownames = "sample_id") |> |
| mutate( |
| healthy_control = str_detect(title, "healthy"), |
| title_date = str_extract(title, "\\d\\d_\\d{2}_\\d{4}"), |
| title_identifier1 = str_extract(title, "(?<=\\d{2}_\\d{2}_\\d{4}_)\\w\\d+"), |
| title_identifier2 = str_extract(title, "\\d+(?=\\])"), |
| sex = clean_char(characteristics_ch1, "^gender:\\s*"), |
| age = as.numeric(clean_char(characteristics_ch1.1, "^age:\\s*")), |
| pneumonia_diagnosis = clean_char(characteristics_ch1.2, "^pneumonia diagnoses:\\s*"), |
| thrombocytopenia = clean_char(characteristics_ch1.3, "^thrombocytopenia:\\s*"), |
| endotype_cohort = clean_char(characteristics_ch1.4, "^endotype_cohort:\\s*"), |
| endotype_class = clean_char(characteristics_ch1.5, "^endotype_class:\\s*"), |
| mortality_28d = as.logical(as.integer(clean_char(characteristics_ch1.6, "^mortality_event_28days:\\s*"))), |
| time_to_event_28d = as.numeric(clean_char(characteristics_ch1.7, "^time_to_event_28days:\\s*")), |
| icu_acquired_infection = clean_char(characteristics_ch1.8, "^icu_acquired_infection:\\s*"), |
| icu_acquired_infection_paired = clean_char(characteristics_ch1.9, "^icu_acquired_infection_paired:\\s*"), |
| diabetes_mellitus = clean_char(characteristics_ch1.10, "^diabetes_mellitus:\\s*"), |
| abdominal_sepsis_or_control = clean_char(characteristics_ch1.11, "^abdominal_sepsis_and_controls:\\s*") |
| ) |> |
| dplyr::select( |
| sample_id, title_identifier1, title_identifier2, healthy_control, sex, |
| age, pneumonia_diagnosis, thrombocytopenia, endotype_cohort, endotype_class, |
| mortality_28d, time_to_event_28d, icu_acquired_infection, icu_acquired_infection_paired, |
| diabetes_mellitus, abdominal_sepsis_or_control |
| ) |
|
|
| stopifnot(gse65682_metadata |> filter(!is.na(endotype_class)) |> count(is.na(mortality_28d)) |> pull(n) == 479) |
|
|
| your_probes_mars <- rownames(exprs(gset)) |
| biocu219_probes <- keys(hgu219.db, keytype = "PROBEID") |
|
|
| length(your_probes_mars) |
| length(biocu219_probes) |
| length(intersect(your_probes_mars, biocu219_probes)) |
| stopifnot(mean(!your_probes_mars %in% biocu219_probes) == 0) |
|
|
| anno_u219 <- AnnotationDbi::select( |
| hgu219.db, |
| keys = your_probes_mars, |
| columns = c("SYMBOL", "ENTREZID", "ENSEMBL", "GENENAME", "UNIPROT"), |
| keytype = "PROBEID" |
| ) |
|
|
| gse65682_feature_metadata <- anno_u219 |> |
| group_by(PROBEID) |> |
| reframe( |
| ENSEMBL = paste(unique(na.omit(ENSEMBL)), collapse = ";"), |
| ENTREZID = dplyr::first(ENTREZID), |
| SYMBOL = dplyr::first(SYMBOL), |
| GENENAME = dplyr::first(GENENAME), |
| UNIPROT = paste(unique(na.omit(UNIPROT)), collapse = ";") |
| ) |> |
| ungroup() |> |
| mutate(across(c(ENSEMBL, UNIPROT), ~ na_if(.x, ""))) |> |
| rename(feature_id = PROBEID) |> |
| right_join(tibble(feature_id = your_probes_mars), by = "feature_id") |
|
|
| stopifnot(nrow(gse65682_feature_metadata) == length(your_probes_mars)) |
| stopifnot(!any(duplicated(gse65682_feature_metadata$feature_id))) |
|
|
| mean(is.na(gse65682_feature_metadata$SYMBOL)) |
|
|
| gse65682_expr_long <- as_tibble(exprs(gset), rownames = "feature_id") |> |
| pivot_longer(-feature_id, names_to = "sample_id", values_to = "value") |> |
| arrange(sample_id, feature_id) |
|
|
| stopifnot(nrow(gse65682_expr_long) == nrow(exprs(gset)) * ncol(exprs(gset))) |
| stopifnot(all(unique(gse65682_expr_long$sample_id) %in% gse65682_metadata$sample_id)) |
| stopifnot(all(unique(gse65682_expr_long$feature_id) %in% gse65682_feature_metadata$feature_id)) |
|
|
| stopifnot(!any(duplicated(gse65682_metadata$sample_id))) |
| stopifnot(nrow(gse65682_metadata) == 802) |
|
|
| dir.create("data/gse65682/parquet", recursive = TRUE, showWarnings = FALSE) |
|
|
| arrow::write_parquet(gse65682_metadata, "data/gse65682/parquet/sample_metadata.parquet") |
| arrow::write_parquet(gse65682_feature_metadata, "data/gse65682/parquet/feature_metadata.parquet") |
| arrow::write_parquet(gse65682_expr_long, "data/gse65682/parquet/expression.parquet") |
|
|
