Hi, everyone! Is there anyone here familiar with or using the RTCGAToolbox package? I found it to be very useful when importing, compiling and exporting data from the Firehose repository. However, I am simply unable to export miRNA data. Here is what I'm doing:
> miOV <- getFirehoseData(dataset="OV", runDate = "20160128", gistic2Date = NULL, clinical = TRUE, miRNAArray = T, forceDownload = T)
And it works fine:
> miOV OV FirehoseData objectStandard run date: 20160128 Analysis running date: N/A Available data types: clinical: A data frame of phenotype data, dim: 591 x 21 miRNAArray: A list of FirehosemRNAArray object(s), length: 1 To export data, use the 'getData' function.
Now, when I try to export it, it gives me the following message:
> miRNAData <- getData(OV_miRNA, "miRNAArray")
Error in .getListData(getElement(object, type), platform) : argument "platform" is missing, with no default
I checked what the acceptable arguments were, and it describes as:
An index for data types that may come from multiple platforms (such as mRNAArray), for GISTIC data, one of the options: 'AllByGene' or 'ThresholdedByGene'
In this case, I checked the platform for this specific set of data, which was performed on Agilent Human miRNA microarray Rel12.0.
I tried adding "Agilent", "Agilent Human miRNA", and other values, but it didn't work.
Would anybody have any idea on how to solve this issue? Thanks!