smile.data.parser.microarray

Class RESParser

java.lang.Object

smile.data.parser.microarray.RESParser

public class RESParser
extends java.lang.Object

ExpRESsion (with P and A calls) file parse. The RES file format is a tab delimited file format that describes a gene expression dataset. The main difference between RES and GCT file formats is the RES file format contains labels for each gene's absent (A) versus present (P) calls as generated by Affymetrix's GeneChip software.

The first line contains a list of labels identifying the samples associated with each of the columns in the remainder of the file. Two tabs (\t\t) separate the sample identifier labels because each sample contains two data values (an expression value and a present/marginal/absent call).

Line format:

Description (tab) Accession (tab) (sample 1 name) (tab) (tab) (sample 2 name) (tab) (tab) ... (sample N name)

For example:

Description Accession DLBC1_1 DLBC2_1 ... DLBC58_0

The second line contains a list of sample descriptions.

Line format:

(tab) (sample 1 description) (tab) (tab) (sample 2 description) (tab) (tab) ... (sample N description)

Example:

MG2000062219AA MG2000062256AA/scale factor=1.2172 ... MG2000062211AA/scale factor=1.1214

The third line contains a number indicating the number of rows in the data table that is contained in the remainder of the file.

Line format:

(# of data rows)

For example:

7129

The remainder of the data file contains data for each of the genes. There is one row for each gene and two columns for each of the samples. The first two fields in the row contain the description and name for each of the genes (names and descriptions can contain spaces since fields are separated by tabs). The description field is optional but the tab following it is not. Each sample has two pieces of data associated with it: an expression value and an associated Absent/Marginal/Present (A/M/P) call. The A/M/P calls are generated by microarray scanning software (such as Affymetrix's GeneChip software) and are an indication of the confidence in the measured expression value.

Line format:

(gene description) (tab) (gene name) (tab) (sample 1 data) (tab) (sample 1 A/P call) (tab) (sample 2 data) (tab) (sample 2 A/P call) (tab) ... (sample N data) (tab) (sample N A/P call)

For example:

AFFX-BioB-5_at (endogenous control) AFFX-BioB-5_at -104 A -152 A ... -44 A

Constructor Summary

Constructors

Constructor and Description
RESParser() Constructor.

Method Summary

Modifier and Type	Method and Description
AttributeDataset	parse(java.io.File file) Parse a RES dataset from given file.
AttributeDataset	parse(java.lang.String path) Parse a RES dataset from given file.
AttributeDataset	parse(java.lang.String name, java.io.File file) Parse a RES dataset from given file.
AttributeDataset	parse(java.lang.String name, java.io.InputStream stream) Parse a RES dataset from an input stream.
AttributeDataset	parse(java.lang.String name, java.lang.String path) Parse a RES dataset from given file.
AttributeDataset	parse(java.lang.String name, java.net.URI uri) Parse a RES dataset from given URI.
AttributeDataset	parse(java.net.URI uri) Parse a RES dataset from given URI.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RESParser

public RESParser()

Constructor.

Method Detail

parse

public AttributeDataset parse(java.net.URI uri)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a RES dataset from given URI.

Throws:

java.io.IOException

java.text.ParseException

parse

public AttributeDataset parse(java.lang.String name,
                              java.net.URI uri)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a RES dataset from given URI.

Parameters:

uri - the URI of data source.

Throws:

java.io.IOException

java.text.ParseException

parse

public AttributeDataset parse(java.lang.String path)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a RES dataset from given file.

Throws:

java.io.IOException

java.text.ParseException

parse

public AttributeDataset parse(java.lang.String name,
                              java.lang.String path)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a RES dataset from given file.

Parameters:

path - the file path of data source.

Throws:

java.io.IOException

java.text.ParseException

parse

public AttributeDataset parse(java.io.File file)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a RES dataset from given file.

Throws:

java.io.IOException

java.text.ParseException

parse

public AttributeDataset parse(java.lang.String name,
                              java.io.File file)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a RES dataset from given file.

Parameters:

file - the file of data source.

Throws:

java.io.IOException

java.text.ParseException

parse

public AttributeDataset parse(java.lang.String name,
                              java.io.InputStream stream)
                       throws java.io.IOException,
                              java.text.ParseException

Parse a RES dataset from an input stream.

Parameters:

name - the name of dataset.

stream - the input stream of data.

Throws:

java.io.IOException

java.text.ParseException