## ----ky1, load-depenencies, results="hide", message=FALSE, warning=FALSE------
library(knowYourCG)
library(sesameData)
sesameDataCache(data_titles=c("genomeInfo.hg38","genomeInfo.mm10",
                  "KYCG.MM285.tissueSignature.20211211",
                  "MM285.tissueSignature","MM285.address",
                  "probeIDSignature","KYCG.MM285.designGroup.20210210",
                  "KYCG.MM285.chromHMM.20210210",
                  "KYCG.MM285.TFBSconsensus.20220116",
                  "KYCG.MM285.HMconsensus.20220116",
                  "KYCG.MM285.chromosome.mm10.20210630"
                  ))

## ----ky2, message=FALSE-------------------------------------------------------
query <- getDBs("MM285.designGroup")[["PGCMeth"]]
head(query)

## ----ky3, fig.width=8, fig.height=5, message=FALSE----------------------------
dbs <- c("KYCG.MM285.chromHMM.20210210",
         "KYCG.HM450.TFBSconsensus.20211013",
         "KYCG.MM285.HMconsensus.20220116",
         "KYCG.MM285.tissueSignature.20211211",
         "KYCG.MM285.chromosome.mm10.20210630",
         "KYCG.MM285.designGroup.20210210")
results_pgc <- testEnrichment(query,databases = dbs,platform="MM285")
head(results_pgc)

## ----ky5, list-data, eval=TRUE, echo=TRUE-------------------------------------
listDBGroups("MM285")

## ----ky6, cache-data, eval=TRUE, warning=FALSE--------------------------------
dbs <- getDBs("MM285.design")

## ----ky7, view-data1, eval=TRUE, warning=FALSE--------------------------------
str(dbs[["PGCMeth"]])

## ----ky7b, eval=FALSE---------------------------------------------------------
# # Load ImprintingDMR database from Zenodo
# dbs_imprinting <- readRDS(url(paste0(
#     "https://zenodo.org/records/18344496/files/",
#     "KYCG.HM450.ImprintingDMR.20220818.rds")))
# 
# # Examine the loaded database
# str(dbs_imprinting)

## ----ky7c, eval=FALSE---------------------------------------------------------
# # Load multiple databases from Zenodo
# 
# urls <- paste0(
#     "https://zenodo.org/records/18344496/files/",
#     c("KYCG.HM450.ImprintingDMR.20220818.rds",
#         "KYCG.HM450.Blacklist.20220304.rds"))
# 
# dbs_multiple <- do.call(c, lapply(urls, function(x) readRDS(url(x))))
# 
# # Examine the loaded database
# str(dbs_multiple)
# 
# # Use these databases in enrichment testing
# results <- testEnrichment(query, dbs_multiple, platform="HM450")

## ----ky8, run-test-single, echo=TRUE, eval=TRUE, message=FALSE----------------
library(SummarizedExperiment)

## prepare a query
df <- rowData(sesameDataGet('MM285.tissueSignature'))
query <- df$Probe_ID[df$branch == "fetal_brain" & df$type == "Hypo"]

results <- testEnrichment(query, "TFBS", platform="MM285")
results %>% dplyr::filter(overlap>10) %>% head

## prepare another query
query <- df$Probe_ID[df$branch == "fetal_liver" & df$type == "Hypo"]
results <- testEnrichment(query, "TFBS", platform="MM285")
results %>% dplyr::filter(overlap>10) %>%
    dplyr::select(dbname, estimate, test, FDR) %>% head

## ----ky9, message=FALSE-------------------------------------------------------
df <- rowData(sesameDataGet('MM285.tissueSignature'))
query <- df$Probe_ID[df$branch == "B_cell"]
head(query)

## ----ky10, fig.width=7, fig.height=6, echo=TRUE, warning=FALSE, message=FALSE----
library(knowYourCG)
library(sesameData)
library(SummarizedExperiment)
query <- names(sesameData_getProbesByGene("Dnmt3a", "MM285"))
results <- testEnrichment(query, 
    buildGeneDBs(query, max_distance=100000, platform="MM285"),
    platform="MM285")
main_stats <- c("dbname","estimate","gene_name","FDR", "nQ", "nD", "overlap")
results[,main_stats]

## ----ky11, warning=FALSE, message=FALSE, fig.width=5, fig.height=4------------
query <- names(sesameData_getProbesByGene("Dnmt3a", "MM285"))
dbs <- c("KYCG.MM285.chromHMM.20210210","KYCG.HM450.TFBSconsensus.20211013",
         "KYCG.MM285.chromosome.mm10.20210630")
results <- testEnrichment(query,databases=dbs,
                          platform="MM285",include_genes=TRUE)
main_stats <- c("dbname","estimate","gene_name","FDR", "nQ", "nD", "overlap")
results[,main_stats] %>% head()

## ----ky12, message=FALSE, eval=FALSE------------------------------------------
# ## prepare query probes
# df <- rowData(sesameData::sesameDataGet('MM285.tissueSignature'))
# query_probes <- df$Probe_ID[df$branch == "fetal_liver" & df$type == "Hypo"]
# 
# ## link them to genes
# genes <- linkProbesToProximalGenes(query_probes, platform = "MM285")$gene_name
# 
# ## use gprofiler2 to test enrichment
# library(gprofiler2)
# gostres <- gprofiler2::gost(genes, organism = "mmusculus")
# head(gostres$result[order(gostres$result$p_value),])
# 

## ----ky13, eval = TRUE,message=FALSE------------------------------------------
df <- rowData(sesameDataGet('MM285.tissueSignature'))
probes <- df$Probe_ID[df$branch == "fetal_liver" & df$type == "Hypo"]
res <- testProbeProximity(probeIDs=probes)
head(res)

## ----session-info-------------------------------------------------------------
sessionInfo()