## ---- 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()