Package 'TCGAWorkflowData'

Data for TCGA Workflow

Description

This experimental data package has the data necessary to follow the TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages. It contains the following files:

• met20SamplesGBMLGGchr9: DNA methylation matrix from Infinium HumanMethylation450 platform for 10 LGG (Lower grade glioma) and 10 GBM (Glioblastoma multiforme). It has only probes in chromossome 9 in order to make the example of the workflow faster

• elmerExample: Contains a DNA methylation matrix (only probes in chromossome 9) and a gene expression matrix for 10 LGG (Lower grade glioma) and 10 GBM (Glioblastoma multiforme) in the required format for to execute the R/Bioconductor ELMER package analysis and a vector identifying which sample belongs to each tumor type.

• biogrid: biogrid information

• maf_lgg_gbm: Mutation annotation files for LGG (Lower grade glioma) and GBM (Glioblastoma multiforme) samples merged into a single matrix. The GDC Somatic Mutation Calling Workflow mutect2 was used to create this MAF files.

• histoneMarks: histone marks specific for brain tissue using from Roadmap database.

• genes_GR: A GRanges Object and a dataframe with gene information (hg19) downloaded from ENSEMBLE database using biomart via TCGAbiolinks

• TCGA_GBM_Transcriptome_20_samples: a matrix with raw expression signal for expression of a gene for 20 GBM (Glioblastoma multiforme) samples

• TCGA_LGG_Transcriptome_20_samples: a matrix with raw expression signal for expression of a gene for 20 LGG (low grade glioma) samples

For more information how to create these objects please read the vignette of this package with the follwing command: browseVignettes("TCGAWorkflowData")

Examples

data("elmerExample")
data("TCGA_LGG_Transcriptome_20_samples")
data("TCGA_GBM_Transcriptome_20_samples")
data("histoneMarks")
data("biogrid")
data("genes_GR")
data("maf_lgg_gbm")

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