sam2excel {siggenes}R Documentation

CSV file of a SAM object


Generates a csv file for a SAM 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.


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


object a SAM 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
ll logical indicating if both the locus 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 exprSet 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


Holger Schwender,

See Also

SAM-class, sam, sam2html

[Package siggenes version 1.4.0 Index]