I am trying to download miRNA expression data for Ovarian Cancer using TCGAbiolinks' GDCquery. I used the commands below few months ago for Prostate cancer dataset and it was working then. It doesn't work for prostate cancer now either.
query <- GDCquery(project = "TCGA-OV",
data.category = "Transcriptome Profiling",
data.type = "miRNA Expression Quantification")
GDCdownload(query)
counts <- GDCprepare(query)
Error in grepl("miRNA", data.type, ignore.case) :
object 'ignore.case' not found
Can anyone help with solving this error? Thanks in advance !
Hi yes, sorry, I did try 'TCGA-OV' and it still gives the same error. Previously, I was also trying to download 'TARGET- AML' hence copy and pasted the wrong code. I will edit my main post.
You might also try curatedTCGAData - it has an advantage of linking assays and clinical/pathological/specimen data in a MultiAssayExperiment. Here I obtain both the miRNA array and sequencing data in one MultiAssayExperiment:
> library(curatedTCGAData)
Loading required package: MultiAssayExperiment
> curatedTCGAData()
Please see the list below for available cohorts and assays
Available Cancer codes:
ACC BLCA BRCA CESC CHOL COAD DLBC ESCA GBM HNSC KICH
KIRC KIRP LAML LGG LIHC LUAD LUSC MESO OV PAAD PCPG
PRAD READ SARC SKCM STAD TGCT THCA THYM UCEC UCS UVM
Available Data Types:
CNACGH CNASeq CNASNP CNVSNP GISTICA GISTICT
Methylation miRNAArray miRNASeqGene mRNAArray
Mutation RNASeq2GeneNorm RNASeqGene RPPAArray
> curatedTCGAData(diseaseCode = "OV")
OV_CNACGH1 OV_CNACGH2
"OV_CNACGH_CGH_hg_244a-20160128.rda" "OV_CNACGH_CGH_hg_415k_g4124a-20160128.rda"
OV_CNASNP OV_CNVSNP
"OV_CNASNP-20160128.rda" "OV_CNVSNP-20160128.rda"
OV_GISTIC_AllByGene OV_GISTIC_ThresholdedByGene
"OV_GISTIC_AllByGene-20160128.rda" "OV_GISTIC_ThresholdedByGene-20160128.rda"
OV_Methylation1 OV_Methylation2
"OV_Methylation_methyl27-20160128.rda" "OV_Methylation_methyl450-20160128.rda"
OV_miRNAArray OV_miRNASeqGene
"OV_miRNAArray-20160128.rda" "OV_miRNASeqGene-20160128.rda"
OV_mRNAArray1 OV_mRNAArray2
"OV_mRNAArray_huex-20160128.rda" "OV_mRNAArray_TX_g4502a-20160128.rda"
OV_mRNAArray3 OV_Mutation
"OV_mRNAArray_TX_ht_hg_u133a-20160128.rda" "OV_Mutation-20160128.rda"
OV_RNASeq2GeneNorm OV_RNASeqGene
"OV_RNASeq2GeneNorm-20160128.rda" "OV_RNASeqGene-20160128.rda"
OV_RPPAArray
"OV_RPPAArray-20160128.rda"
> curatedTCGAData(diseaseCode = "OV", assays = c("miRNAArray", "miRNASeqGene"), dry.run = FALSE)
snapshotDate(): 2018-05-08
snapshotDate(): 2018-05-08
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
‘/Users/lwaldron//.ExperimentHub/843’
harmonizing input:
removing 8204 sampleMap rows not in names(experiments)
removing 25 colData rownames not in sampleMap 'primary'
A MultiAssayExperiment object of 2 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 2:
[1] OV_miRNAArray-20160128: SummarizedExperiment with 821 rows and 573 columns
[2] OV_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 461 columns
Features:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample availability DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
>
Thanks for this solution. I tried it and I am able to download the miRseq data, but it seems like the data was curated in 2016 and has not been updated since? As I am able to download mRNA sequencing data from TCGAbiolinks, I wanted to compare their data and curatedTCCGAData's mRNA seq data, however I get another error while trying to download the data:
data <- curatedTCGAData(diseaseCode = 'OV', assays =c('mRNAArray3'), dry.run = F)
Error in .searchFromInputs(assays, assaysAvail) :
No matches found, modify search criteria
mRNAArray3 isn't one of the allowable assay types (mRNAArray is).
curatedTCGAData provides the final Firehose pipeline snapshot. While GDC
provides newer processing for some assays, there are no new data.
>
Hello,
There is no TARGET-OV in GDC. The code should be:
query <- GDCquery(project = "TCGA-OV", data.category = "Transcriptome Profiling", data.type = "miRNA Expression Quantification") GDCdownload(query) counts <- GDCprepare(query)Hi yes, sorry, I did try 'TCGA-OV' and it still gives the same error. Previously, I was also trying to download 'TARGET- AML' hence copy and pasted the wrong code. I will edit my main post.