In MarzyUnicz/MMRFBiolinks:

library(MMRFBiolinks)

library(TCGAbiolinks)
library(SummarizedExperiment)
library(dplyr)
library(DT)

Useful information

Different sources of clinical data

MMRF-Compass clinical data can be retrieved from two different sources: - **GDC Clinical information**: MMRF-Commpass clinical information download from GDC database; - **MMRF-Commpass Clinical information**: Clinical information downloaded directly from MMRF-Commpass Researcher Gateway has more information compared to the previous dataset (e.g Best overall response). So the previous one is only a subset of this. The user can download this dataset from MMRF-Commpass Researcher Gateway and import it as a dataframe into R environment.

GDC Clinical information

In this example we will fetch clinical GD data (same as showed in the GDC data portal).

clinical <- MMRFqueryGDC_clinic(type = "clinical")

clinical %>% head %>% datatable(options = list(scrollX = TRUE, keys = TRUE))

MMRF-Commpass Clinical information

In this example we will fetch clinical MMRF-Commpass data (after having imported into our own R environment).

clinMMGateway %>% datatable(options = list(scrollX = TRUE, keys = TRUE))

MarzyUnicz/MMRFBiolinks documentation built on May 28, 2020, 4:08 a.m.