fileToXML {AnnBuilder}R Documentation

A function to convert a text file to XML.

Description

This function takes a text file and then converts the data contained by the file to an XML file. The XML file contains an Attr and a Data node. The Attr node contains mata-data and the Data node contains real data from the original file.

Usage

fileToXML(targetName, outName, inName, idColName, colNames,
multColNames, typeColNames,  multSep = ";", typeSep = ";", fileSep =
"\t", header = FALSE, isFile = TRUE, organism = "human",version = "1.0.0")

Arguments

outName outNameA character string for the name of xml file to be produced. If the name does not contain a full path, the current working directory will be the default
inName inName A character string for the name of the input file to be written to an XML document
idColName idColName A character string for the name of the column in the input file where ids of the target of annotation are
colNames colNames A vector of character strings for the name of data columns in the original file.
targetName targetName A character string that will be used as an internal name for the meta-data to show the target of the annotation (e.g. U95, U6800.
version version A character string or number indicating the version of the system used to build the xml file.
multColNames multColNames A vector of character strings for the name of data columns that may contain multiple items separated by a separator specified by parameter multSep.
typeColNames typeColNames A vector of character strings for data columns in the original data that may contain type information append to the real data with a separator defined by parameter typeSep (e.g. "aGeneName;Officila").
multSep mutlSep A character string for the separator used to separate multiple data items within a data column of the original file.
typeSep typeSep A character string for the separator used to separate the real data and type information within a column of the original data.
fileSep fileSep A character string specifying how data columns are separated in the original file (e.g. sep = "t" for tab delimited.
organism organism A character string for the name of the organism of interests
header header A boolean that is set to TRUE if the original file has a header row or FALSE otherwise.
isFile isFile A boolean that is set to TRUE if parameter fileName is the name of an existing file and FALSE if fileName is a R object contains the data

Details

The original text file is assumed to have rows with columns separated by a separator defined by parameter sep. MultCol are used to define data columns that capture the one to many relationships between data. For example, a given AffyMetrix id may be associated with several GenBank accession numbers. In a data set with AffyMetrix ids as one of the data columns, the accession number column will be a element in multCol with a separator separating individual accession numbers (e.g. X00001,X00002,U0003... if the separator is a ",").

As gene name and gene symbol can be "Official" or "Preferred", a type information is attached to a gene name or symbol that is going to be the value for attribute type in the resulting XML file (e.g. XXXX;Official if the separator is ";").

Value

This function does not return any value. The XML file will be stored as a file.

Note

This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinfomatics functionalities through R.

Author(s)

Jianhua (John) Zhang

References

http://www.bioconductor.org/datafiles/dtds/annotate.dtd

See Also

ABPkgBuilder

Examples

# Create a text file
aFile <- as.data.frame(matrix(c(1:9), ncol = 3))

#Write to an XML file
if(interactive()){
    fileToXML("notReal", outName = "try.xml", inName = aFile, idColName =
    "AFFY", colNames = c("AFFY", "LOCUSID", "UNIGENE"), multColNames = NULL,
    typeColNames = NULL,  multSep = ";", isFile = FALSE)

    #Show the XML file
    readLines("try.xml")

    # Clearn up
    unlink("try.xml")
}

[Package AnnBuilder version 1.4.21 Index]