I want to extract Tissue and diagnostic slides images from TCGA. I want to obtain normal slides, tissue slides and diagnostic slides labelled separately. Using data retrieving tools, I get svs format images and I have to then extract images from it for which I cannot find a code and also, the images coming out are not labelled for the sample type.
I tried using this code in R : query <- GDCquery(project = "TCGA-CHOL", data.category = "Biospecimen", data.type = "Slide Image", data.format = "SVS", experimental.strategy="Tissue Slide", sample.type ="Primary Tumor")
but sample.type gives me the error ~ Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent OR Error in checkBarcodeDefinition(sample.type) : Primary Solid Tumor was not found. Please select a difinition from the table above
Please explain to me how can I obtain the 3 three types of images- diagnostic, normal and tissue for each patient of TCGA-CHOL and how do I open them for analysis in R or Python and the image formats used for the same.
And if I use data retriever, how do I get sample type for each of the file and how do I work with the svs file?