In MarzyUnicz/MMRFBiolinks:

library(TCGAbiolinks)
library(MMRFBiolinks)

library(SummarizedExperiment)
library(dplyr)

GDCquery Function

Data Search

MMRFBiolinks relies on the usage of TCGABiolinks functions among which TCGAbiolinks::GDCquery function for searching MMRF-COMMPASS data available at GDC Data Portal. [TCGAbiolinks package](https://bioconductor.org/packages/TCGAbiolinks/) which should be consulted for more detailed information.

GDCquery arguments

The useful arguments for searching MMRF-CoMMpass Project 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.type in MMRF-COMPASS Project are:

sample_type.code|sample_type.def -----|----- 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

Example:

library(DT)
query.mm<-GDCquery(project = "MMRF-COMMPASS",
                    data.category = "Transcriptome Profiling",
                    data.type = "Gene Expression Quantification",
                    workflow.type="HTSeq - FPKM",
                    sample.type="Primary Blood Derived Cancer - Peripheral Blood")

getResults(query.mm, cols = c("cases.submitter_id","sample_type","cases")) %>% DT::datatable(options = list(scrollX = TRUE, keys = TRUE))

Barcode options

Example:

library(DT)
query.mm<-GDCquery(project = "MMRF-COMMPASS",
                    data.category = "Transcriptome Profiling",
                    data.type = "Gene Expression Quantification",
                    workflow.type="HTSeq - FPKM",
                    barcode = c("MMRF_2473","MMRF_2111",
                                "MMRF_2362","MMRF_1824",
                                "MMRF_1458","MRF_1361",
                                "MMRF_2203","MMRF_2762",
                                "MMRF_2680","MMRF_1797"))

getResults(query.mm, cols = c("cases.submitter_id","sample_type","cases")) %>% datatable(options = list(scrollX = TRUE, keys = TRUE))

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