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SAGx (version 1.46.0)

R2BASE: Produces a BASE file

Description

The function produces a BASE file for import to Gene Data Viewer.

Usage

R2BASE(context.data = clingen, sample.ids = AZID, expression.data = dats, 
annotation = annots, out = "u:/temp/temp.base")

Arguments

context.data
e.g. a clinical database
sample.ids
Sample Ids, that names the columns of the expression data.
expression.data
a matrix with the gene expression data, samples correspond to columns and probesets to rows. It is assumed that probeset identifiers are found in the first column.
annotation
annotations of the probesets, i.e. the rows in the expression.data. It is assumed that probeset identifiers are found in the first column.
out
the output file including path

Value

  • The file produced complies with an old BASE format. However, none of these formats are documented , as far as I know. So, essentially this function defines a data format that can be read by e.g. Gene Data Viewer.