CSV file of a SAM or an EBAM object

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Description

Generates a csv file for either a SAM or an EBAM object for the use in Excel. This csv file can contain general information as the number of differentially expressed genes and the estimated FDR, and gene-specific information on the differentially expressed genes.

Usage

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 sam2excel(object, delta, file, excel.version=1, n.digits = 3, what = "both", entrez = FALSE,
        chip = "", quote = FALSE)
        
 ebam2excel(object, delta, file, excel.version=1, n.digits = 4, what = "both", entrez = FALSE,
        chip = "", quote = FALSE)

Arguments

object

either a SAM or an EBAM object.

delta

a numerical value specifying the Delta value.

file

character string naming the file in which the output should be stored. Must have the suffix ".csv".

excel.version

either 1 or 2. If excel.version=1 (default) a csv file for the use in an Excel version with American standard settings (sep="," and dec=".") will be generated. If excel.version=2 a csv file for the European standard setting (sep=";" and dec=",") will be generated.

n.digits

integer specifying the number of decimal places used in the output.

what

either "both", "stats" or "genes". If "stats" general information will be shown. If "genes" gene-specific information will be given. If "both" both general and gene-specific information will be shown.

entrez

logical indicating if both the Entrez links and the symbols of the genes will be added to the output.

chip

character string naming the chip type used in this analysis. Must be specified as in the meta-data section of Bioconductor (e.g., "hgu133a" for the Affymetrix HG-U133A chip). Only needed if ll = TRUE. If the argument data in sam(data, cl, ...) has been specified by an ExpressionSet object chip need not to be specified.

quote

logical indicating if character strings and factors should be surrounded by double quotes. For details see write.table.

Author(s)

Holger Schwender, holger.schw@gmx.de

See Also

sam, sam2html, ebam, ebam2html

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