In MarzyUnicz/MMRFBiolinksX:

library(MMRFBiolinksX)

# This code chunk simply makes sure that all the libraries used here are installed, it will not be shown in the report (notice echo = FALSE).
packages <- c("knitr", "dplyr", "plotly","DT","TCGAbiolinks","SummarizedExperiment")
if ( length(missing_pkgs <- setdiff(packages, rownames(installed.packages()))) > 0) {
  message("Installing missing package(s): ", paste(missing_pkgs, collapse = ", "))
  install.packages(missing_pkgs)
}

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

Searching arguments

GDCquery in function in TCGAbiolinks package allows to search GDC data using arguments. The useful arguments for searching MMRF-Projects data are:

Arguments | Description -----|----- Data.category| A valid data category in the list below Data.type| A data type to filter the files to download Workflow.type| GDC workflow type Access| Filter by access type. Possible values: controlled experimental_strategy| Filter to experimental strategy barcode| A list of barcodes to filter the files to download sample.type| A sample type to filter the files to download

The arguments options for filtering MMRF-COMMPASS data are listed below:

| Data.category | Data.type | Workflow Type | Access | experimental_strategy
|----------------------------- | ----------------------------------- | ------------------------------- | -------------------- |------------------------ | | Transcriptome Profiling | Gene Expression Quantification | HTSeq - Counts | Open / Controlled | RNA-Seq |
| | | HTSeq - FPKM-UQ | Open / Controlled | RNA-Seq |
| | | HTSeq - FPKM | Open / Controlled | RNA-Seq |
| | | STAR - Counts | Open / Controlled | RNA-Seq | | | Splice Junction Quantification | STAR - Counts | Open / Controlled | RNA-Seq |
| Simple Nucleotide Variation | Raw Simple Somatic Mutation | MuSE | Controlled | WXS | | | | SomaticSniper | Controlled | WXS | | | | VarScan2 | Controlled | WXS | | | | Pindel | Controlled | WXS | | | | MuTect2 | Controlled | WXS | | | Annotated Somatic Mutation | MuSE Annotation | Controlled | WXS | | | | VarScan2 Annotation | Controlled | WXS | | | | Pindel Annotation | Controlled | WXS | | | | MuTect2 Annotation | Controlled | WXS | | | | SomaticSniper Annotation | Controlled | WXS | | Sequencing Reads | Aligned Reads | BWA with Mark Duplicates and BQSR | Controlled | WXS / RNA-Seq / WGS | | | | STAR 2-Pass Genome | Controlled | WXS / RNA-Seq / WGS | | | | STAR 2-Pass Transcriptome | Controlled | WXS / RNA-Seq / WGS |

sample.type options

The options for the field sample.typein MMRF-COMPASS Project are:

MMRFBiolinksX:::getSampleTypes()

sample_type.def|sample_type.code -----|----- TRBM|Recurrent Blood Derived Cancer - Bone Marrow TBM|Primary Blood Derived Cancer - Bone Marrow NB|Blood Derived Normal TB|Primary Blood Derived Cancer - Peripheral Blood TRB|Recurrent Blood Derived Cancer - Peripheral Blood

Barcode options

Example:

GDCquery(project = "MMRF-COMMPASS",
                    data.category = "Transcriptome Profiling",
                    data.type = "Gene Expression Quantification",
                    workflow.type="HTSeq - FPKM",
                    barcode = c("MMRF_2473","MMRF_2111"))

MarzyUnicz/MMRFBiolinksX documentation built on April 7, 2020, 1:05 p.m.