songtr / firebrowser

An R client for broads firehose pipeline, providing TCGA data sets

#FirebrowseR

FirebrowseR is a R client for Broads Firehose Web API, which is serving data generated by the Firehose Pipeline. Note: This pipeline processes TCGA date sets.

Why should I use FirebrowseR?

Short: Directly get TCGA/Firhose data into R.

Long: Whoever used the TCGA downloads should have noticed that the formats are never the same, even for data sets of the same type. Broads Firehose API resolves these issues. You directly receive JSON, CSV or TSV output. At this point FirebrowseR is entering the game, directly connecting your R session to the API and allowing you to query all data sets. You receive standardized data frames or json objects (requiring the jsonlite package).

How do I get it?

Short: devtools::install_github("mariodeng/FirebrowseR")

Long: The command above is executed from your R session and requires the devtools package to be installed. If it's not already installed, please do so by executing install.packages("devtools"). Later, when the API has droped its beta status, there will be a CRAN release.

How do I use it

Short:

require(FirebrowseR)
mRNA.Exp = Samples.mRNASeq(format = "csv",
                           gene = c("PTEN", "RUNX1"),
                           tcga_participant_barcode = c("TCGA-GF-A4EO",
                                                        "TCGA-AC-A2FG")
                           )
mRNA.Exp[, c("tcga_participant_barcode", "expression_log2", "z.score")]

  tcga_participant_barcode expression_log2     z.score
1             TCGA-AC-A2FG       11.061951  0.05874861
2             TCGA-AC-A2FG       12.356552  0.50702959
3             TCGA-GF-A4EO       10.461968  0.04383352
4             TCGA-GF-A4EO        9.886488 -0.18698327

Long:

Please see vignettes/FirebrowseR.Rmd