SRA submisison

This script prepares the submisssion to SRA. We will use mbtools to facilitate this.

library(mbtools)

files <- find_read_files(
    "data/raw", 
    pattern = mbtools:::simple_pattern, annotations = mbtools:::simple_annotations)
print(files)

And let’s have a look

files

Not much going on here so we will also load the metadata.

classes <- c(microbiome_id = "character")
cohort <- list(
    no_loss = fread("no_weight_loss.csv", colClasses = classes)[, "group" := "no weight loss"],
    loss = fread("successful_weight_loss.csv", colClasses = classes)[, "group" := "weight loss"]
) %>% rbindlist()
cohort[, "state" := c("before", "after")[order(days_in_program)], by = "public_client_id"]
cohort