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

## ----setup--------------------------------------------------------------------
library(TMExplorer)

## -----------------------------------------------------------------------------
res = queryTME(metadata_only = TRUE)

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(head(res[[1]][,1:5]))

## -----------------------------------------------------------------------------
res = queryTME(tumour_type = 'Breast cancer', metadata_only = TRUE)[[1]]

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(head(res[,1:5]))

## -----------------------------------------------------------------------------
res = queryTME(geo_accession = "GSE81861")

## ---- eval=FALSE--------------------------------------------------------------
#  View(counts(res[[1]]))

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(head(counts(res[[1]])[,1:2]))

## -----------------------------------------------------------------------------
metadata(res[[1]])$pmid

## ---- eval=FALSE--------------------------------------------------------------
#  res = queryTME(has_truth = TRUE)

## ---- eval=FALSE--------------------------------------------------------------
#  View(colData(res[[1]]))

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(head(colData(res[[1]])))

## ---- eval=FALSE--------------------------------------------------------------
#  res = queryTME(has_truth = TRUE, has_signatures = TRUE)
#  View(metadata(res[[1]])$signatures)

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(metadata(res[[1]])$signatures[,1:3])

## ---- eval=FALSE--------------------------------------------------------------
#  res = queryTME(geo_accession = "GSE72056")[[1]]
#  saveTME(res, '~/Downloads/GSE72056')

## -----------------------------------------------------------------------------
sessionInfo()