R2BASE: Produces a BASE file

In SAGx: Statistical Analysis of the GeneChip

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.

Author(s)

Per Broberg

SAGx documentation built on Nov. 8, 2020, 8:18 p.m.