Binary mutation data format
Hi I want to run a package named DawnRank in R. This package has some data requirements and file format. One of these requirements is a mutation file that the rows represent the genes and the columns represent the sample IDs and the mutation for each gene in each samples are binary (0,1) (you could see an example of this file here). I am not very familiar with the TCGA file formats and I couldn't found such data format. Does anyone know how can I find or create this file format?
Thank you for your help.
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igor
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Shamim Sarhadi
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Shamim Sarhadi
1 answer
I think the matrix you are looking for can be found at Xena gene level non-silent mutations.
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You're going to need to custom-process TCGA data to get to this matrix. Linkedomics has this sort of matrices available for download (example: BRCA dataset), although the datasets were cleaned to remove genes that were mutated in fewer than 20% of samples (I think). You may want to email them to find out what sort of filters were used.