Thanks! Will do. On Sun, Aug 26, 2018 at 5:37 PM Bert Gunter <bgunter.4...@gmail.com> wrote:
> You should probably post this on the Bioconductor list rather then here, > as you would more likely find the expertise you seek there. You are using > Bioconductor packages after all. > > https://support.bioconductor.org/ > > Cheers, > Bert > > > On Sun, Aug 26, 2018 at 2:09 PM Spencer Brackett < > spbracket...@saintjosephhs.com> wrote: > >> Good evening, >> >> I am attempting to run the following analysis on TCGA data, however >> something is being reported as an error in my arguments... any ideas as to >> what is incorrect in the following? Thanks! >> >> 1 library(TCGAbiolinks) >> 2 >> 3 # Download the DNA methylation data: HumanMethylation450 LGG and GBM. >> 4 path <– "." >> 5 >> 6 query.met <– TCGAquery(tumor = c("LGG","GBM"),"HumanMethylation450", >> level = 3) >> 7 TCGAdownload(query.met, path = path ) >> 8 met <– TCGAprepare(query = query.met,dir = path, >> 9 add.subtype = TRUE, add.clinical = TRUE, >> 10 summarizedExperiment = TRUE, >> 11 save = TRUE, filename = "lgg_gbm_met.rda") >> 12 >> 13 # Download the expression data: IlluminaHiSeq_RNASeqV2 LGG and GBM. >> 14 query.exp <– TCGAquery(tumor = c("lgg","gbm"), platform = >> "IlluminaHiSeq_ >> RNASeqV2",level = 3) >> 15 >> 16 TCGAdownload(query.exp,path = path, type = "rsem.genes.normalized_ >> results") >> 17 >> 18 exp <– TCGAprepare(query = query.exp, dir = path, >> 19 summarizedExperiment = TRUE, >> 20 add.subtype = TRUE, add.clinical = TRUE, >> 21 type = "rsem.genes.normalized_results", >> 22 save = T,filename = "lgg_gbm_exp.rda") >> >> To download data on DNA methylation and gene expression… >> >> 1 library(summarizedExperiment) >> 2 # get expression matrix >> 3 data <– assay(exp) >> 4 >> 5 # get sample information >> 6 sample.info <– colData(exp) >> 7 >> 8 # get genes information >> 9 genes.info <– rowRanges(exp) >> >> Following stepwise procedure for obtaining GBM and LGG clinical data… >> >> 1 # get clinical patient data for GBM samples >> 2 gbm_clin <– TCGAquery_clinic("gbm","clinical_patient") >> 3 >> 4 # get clinical patient data for LGG samples >> 5 lgg_clin <– TCGAquery_clinic("lgg","clinical_patient") >> 6 >> 7 # Bind the results, as the columns might not be the same, >> 8 # we will plyr rbind.fill , to have all columns from both files >> 9 clinical <– plyr::rbind.fill(gbm_clin ,lgg_clin) >> 10 >> 11 # Other clinical files can be downloaded, >> 12 # Use ?TCGAquery_clinic for more information >> 13 clin_radiation <– TCGAquery_clinic("lgg","clinical_radiation") >> 14 >> 15 # Also, you can get clinical information from different tumor types. >> 16 # For example sample 1 is GBM, sample 2 and 3 are TGCT >> 17 data <– TCGAquery_clinic(clinical_data_type = "clinical_patient", >> 18 samples = c("TCGA-06-5416-01A-01D-1481-05", >> 19 "TCGA-2G-AAEW-01A-11D-A42Z-05", >> 20 "TCGA-2G-AAEX-01A-11D-A42Z-05")) >> >> >> # Searching idat file for DNA methylation >> query <- GDCquery(project = "TCGA-GBM", >> data.category = "Raw microarray data", >> data.type = "Raw intensities", >> experimental.strategy = "Methylation array", >> legacy = TRUE, >> file.type = ".idat", >> platform = "Illumina Human Methylation 450") >> >> **Repeat for LGG** >> >> To access mutational information concerning TMZ methylation… >> >> > mutation <– TCGAquery_maf(tumor = "lgg") >> 2 Getting maf tables >> 3 Source: https://wiki.nci.nih.gov/display/TCGA/TCGA+MAF+Files >> 4 We found these maf files below: >> 5 MAF.File.Name >> 6 2 hgsc.bcm.edu_LGG.IlluminaGA_DNASeq.1.somatic.maf >> 7 >> 8 3 LGG_FINAL_ANALYSIS.aggregated.capture.tcga.uuid.curated.somatic.maf >> 9 >> 10 Archive.Name Deploy.Date >> 11 2 hgsc.bcm.edu_LGG.IlluminaGA_DNASeq_automated.Level_2.1.0.0 >> 10-DEC-13 >> 12 3 broad.mit.edu_LGG.IlluminaGA_DNASeq_curated.Level_2.1.3.0 >> 24-DEC-14 >> 13 >> 14 Please, select the line that you want to download: 3 >> >> **Repeat this for GBM*** >> >> Selecting specified lines to download… >> >> 1 gbm.subtypes <− TCGAquery_subtype(tumor = "gbm") >> 2 lgg.subtypes <− TCGAquery_subtype(tumor = "lgg”) >> >> >> >> Downloading data via the Bioconductor package RTCGAtoolbox… >> >> library(RTCGAToolbox) >> 2 >> 3 # Get the last run dates >> 4 lastRunDate <− getFirehoseRunningDates()[1] >> 5 lastAnalyseDate <− getFirehoseAnalyzeDates(1) >> 6 >> 7 # get DNA methylation data, RNAseq2 and clinical data for LGG >> 8 lgg.data <− getFirehoseData(dataset = "LGG", >> 9 gistic2_Date = getFirehoseAnalyzeDates(1), runDate = lastRunDate, >> 10 Methylation = TRUE, RNAseq2_Gene_Norm = TRUE, Clinic = TRUE, >> 11 Mutation = T, >> 12 fileSizeLimit = 10000) >> 13 >> 14 # get DNA methylation data, RNAseq2 and clinical data for GBM >> 15 gbm.data <− getFirehoseData(dataset = "GBM", >> 16 runDate = lastDate, gistic2_Date = getFirehoseAnalyzeDates(1), >> 17 Methylation = TRUE, Clinic = TRUE, RNAseq2_Gene_Norm = TRUE, >> 18 fileSizeLimit = 10000) >> 19 >> 20 # To access the data you should use the getData function >> 21 # or simply access with @ (for example gbm.data@Clinical) >> 22 gbm.mut <− getData(gbm.data,"Mutations") >> 23 gbm.clin <− getData(gbm.data,"Clinical") >> 24 gbm.gistic <− getData(gbm.data,"GISTIC") >> >> >> >> >> >> >> Genomic Analysis/Final data extraction: >> >> Enable “getData” to access the data >> >> Obtaining GISTIC results… >> >> 1 # Download GISTIC results >> 2 gistic <− getFirehoseData("GBM",gistic2_Date ="20141017" ) >> 3 >> 4 # get GISTIC results >> 5 gistic.allbygene <− gistic@GISTIC@AllByGene >> 6 gistic.thresholedbygene <− gistic@GISTIC@ThresholedByGene >> >> Repeat this procedure to obtain LGG GISTIC results. >> >> ***Please ignore the 'non-coded' text as they are procedural >> steps/classifications*** >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
