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BIMIB-DISCo / VERSO

Viral Evolution ReconStructiOn (VERSO). The manuscript of the method is available at: https://www.cell.com/patterns/fulltext/S2666-3899(21)00022-2
https://bimib-disco.github.io/VERSO/
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sample_info_matrix.csv #6

Closed AndreaAguadoM closed 2 years ago

AndreaAguadoM commented 2 years ago

Good morning

I am still struggling with the VERSO step 2 inputs. Specifically, this time I got stuck on the sample_info_matrix.csv. Specifically, I do not understand the meaning of the Attribute_1 and Attribute_2 columns, since i do not understand which information they add to the table.

About this same matrix: Does the Column genotype refer to the inference$C VERSO step 1 output?

Thanks in advance!

DavideMaspero commented 2 years ago

Dear Andrea,

Attribute_1 and _2 refer to optional columns to store other sample metadata. The only two mandatory columns are "Genotype" and "Selected." The values in the former correspond to the genotype assignment, which you can easily obtain with a command like this as.numeric(gsub(x=inference$C, pattern='G', replacement=''))

The values of the second can all be 1 if all samples have been selected.

Best regards, Davide Maspero