## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(biocohort)

## -----------------------------------------------------------------------------
dir <- tempfile()
dir.create(dir)
writeLines(
  c(
    "subject_id,species,genotype,sex,assay,sample_id,role,fastq_1,fastq_2",
    "R1,rat,WT,F,wes,T1,tumor,t1_R1.fq.gz,t1_R2.fq.gz",
    "R1,rat,WT,F,wes,N1,normal,n1_R1.fq.gz,n1_R2.fq.gz",
    "R2,rat,KO,M,wes,T2,tumor,t2_R1.fq.gz,t2_R2.fq.gz",
    "R2,rat,KO,M,wes,N2,normal,n2_R1.fq.gz,n2_R2.fq.gz"
  ),
  file.path(dir, "manifest.csv")
)

parsed <- read_manifest(file.path(dir, "manifest.csv"))
parsed$subject_tbl
parsed$sample_map

## -----------------------------------------------------------------------------
cohort <- cohort_new(parsed$subject_tbl, parsed$sample_map)
cohort

## -----------------------------------------------------------------------------
wide <- data.frame(
  subject_id = c("R1", "R2"),
  species = "rat",
  wes_tumor_id = c("T1", "T2"),
  wes_normal_id = c("N1", "N2"),
  stringsAsFactors = FALSE
)

id_cols <- data.frame(
  column = c("wes_tumor_id", "wes_normal_id"),
  assay = c("wes", "wes"),
  role = c("tumor", "normal"),
  stringsAsFactors = FALSE
)

manifest_from_wide(wide, id_cols)

## -----------------------------------------------------------------------------
subjects(cohort)
samples(cohort, assay = "wes")
completeness(cohort, wide = TRUE)

## -----------------------------------------------------------------------------
cohort_filter(cohort, genotype == "KO")

## -----------------------------------------------------------------------------
sample_sheet_templates()
sample_sheet(cohort, template = "nf-core/sarek", assay = "wes")

## -----------------------------------------------------------------------------
spec <- analysis_spec_new(
  name = "somatic_vars",
  assay = "wes",
  level = "pair",
  path_template = file.path(dir, "{pair_id}.tsv")
)
cohort <- analysis_register(cohort, spec)
analysis_list(cohort)

## -----------------------------------------------------------------------------
cohort_save(cohort, file.path(dir, "cohort.rds"))
reread <- cohort_read(file.path(dir, "cohort.rds"))
identical(subjects(cohort), subjects(reread))