How to: Write data as a tab-delimited text file

Write data as a tab-delimited text file

Author: Henrik Bengtsson
Created on: 2010-04-22
Last updated: 2010-04-23

Warning: Consider the writeDataFrame() methods to be in alpha version. This means that their API as well as the generated file format might change in a future release. We make it available due to popular demand. /HB 2010-04-23

Data sets and data files are fundamental concepts in the aroma framework, where a data set contains multiple data files in structured directories. There exist multiple methods for extracting signals, that is, reading signals into memory, from the data set or individual data files. For more information, see the 'How tos' section. However, in some cases there is a need to export the data as tab-delimited text files to be imported in other software tools. In this section, we will describe how to write the data to tab-delimited text files. It is possible to generate either (i) one output file per data file, or (ii) one output file for the whole data set.

The writeDataFrame() method takes either a single file or a data set as its first argument. In addition to this, there are various arguments, where maybe the most important one, argument 'columns', specifies which columns the generated text file should contain. For example:

dfTxt <- writeDataFrame(ds, columns="*");

will generate a tab-delimited file with one column per signal field (typically one field per file), where as:

dfTxt <- writeDataFrame(ds, columns=c("unitName", "*"));

will in addition to the above insert a column (first column) with unit names, which are obtained from the unit names file (e.g. the CDF file). Similarly, if one do:

dfTxt <- writeDataFrame(ds, columns=c("unitName", "chromosome", "position", "*"));

the second and third columns will contain chromosome and position information for each unit (loci), which are obtained from the UGP file.

One data file per tab-delimited text file

Example: Export a single data file as a tab-delimited text file with annotation data added

dataSet <- "HapMap270,6.0,CEU,testSet";
tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY";
chipType <- "GenomeWideSNP_6";

ds <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, chipType=chipType);
print(ds);

Name: HapMap270

Tags: 6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY

Full name: HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY

Number of files: 3

Names: NA06991, NA06993, NA07000 [3]

Path (to the first file): ../../../Documents/My Data/totalAndFracBData/HapMap270

,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6

Total file size: 21.53 MB

RAM: 0.00MB

AromaUnitTotalCnBinarySet:
Name: HapMap270
Tags: 6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
Full name: HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
Number of files: 3
Names: NA06991, NA06993, NA07000 [3]
Path (to the first file): totalAndFracBData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
Total file size: 21.53 MB
RAM: 0.00MB

df <- getFile(ds, 2);
print(df);

AromaUnitTotalCnBinaryFile:
Name: NA06993
Tags: total
Full name: NA06993,total
Pathname: totalAndFracBData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/NA06993,total.asb
File size: 7.18 MB (7526121 bytes)
RAM: 0.00 MB
Number of data rows: 1881415
File format: v1
Dimensions: 1881415x1
Column classes: double
Number of bytes per column: 4
Footer: <createdOn>20100422 17:46:03 CEST</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType>
<srcFile><srcDataSet>HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY</srcDataSet><srcChipType>GenomeWideSNP_6,Full,monocell</srcChipType>
<srcFullName>NA06993,chipEffects</srcFullName>
<srcChecksum>1b7625d385394f42f5b31aa988ff43a1</srcChecksum></srcFile>
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full

# Also export a column containing the unit names.
dfTxt <- writeDataFrame(df, columns=c("unitName", "chromosome", "position", "*"));
print(dfTxt);

TabularTextFile:
Name: NA06993
Tags: total
Full name: NA06993,total
Pathname: totalAndFracBData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/NA06993,total.txt
File size: 62.35 MB (65376366 bytes)
RAM: 0.01 MB
Number of data rows: NA
Columns [4]: 'unitName', 'chromosome', 'position', 'NA06993,total'
Number of text lines: NA

data <- readDataFrame(dfTxt, rows=1010:1024);
print(data);

unitName chromosome position NA06993,total

1010 SNP_A-2001589 1 34110291 1022.368

1011 SNP_A-2001596 1 34119149 4317.809

1012 SNP_A-2001598 1 34119693 3229.630

1013 SNP_A-2001642 1 34170728 6060.184

1014 SNP_A-2001643 1 34172791 3469.545

1015 SNP_A-4268291 1 34179429 1953.738

1016 SNP_A-2001684 1 34204360 1353.817

1017 SNP_A-4214101 1 34204556 3615.931

1018 SNP_A-2001700 1 34211296 1784.901

1019 SNP_A-2001835 1 34287073 2973.341

1020 SNP_A-2001840 1 34306289 2415.758

1021 SNP_A-4214120 1 34357252 2631.183

1022 SNP_A-2001896 1 34377866 6363.690

1023 SNP_A-4268333 1 34436399 1606.675

1024 SNP_A-2002002 1 34519557 1946.391

A whole data set per tab-delimited text file

Warning: When writing all of the data available in a data set to a single file, there is no limitation in how large the generated file can be, that is, the more data files there are in the data set, the larger the generated file will be. Some file systems have an upper limit on how large a file can be. Transferring large files is cumbersome. Because of this, we recommend to generate one file per data file.

Example: Export all data of a data set to a tab-delimited text file with annotation data added

dataSet <- "HapMap270,6.0,CEU,testSet";
tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY";
chipType <- "GenomeWideSNP_6";

ds <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, chipType=chipType);
print(ds);

AromaUnitTotalCnBinarySet:

Name: HapMap270

Tags: 6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY

Full name: HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY

Number of files: 3

Names: NA06991, NA06993, NA07000 [3]

Path (to the first file): ../../../Documents/My Data/totalAndFracBData/HapMap270

,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6

Total file size: 21.53 MB

RAM: 0.00MB

# Also export a column containing the unit names.
dfTxt <- writeDataFrame(ds, columns=c("unitName", "chromosome", "position", "*"));
print(dfTxt);

TabularTextFile:
Name: HapMap270
Tags: 6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
Full name: HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
Pathname: totalAndFracBData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY.txt
File size: 107.86 MB (113103874 bytes)
RAM: 0.01 MB
Number of data rows: NA
Columns [6]: 'unitName', 'chromosome', 'position', 'NA06991,total', 'NA06993,total', 'NA07000,total'
Number of text lines: NA

data <- readDataFrame(dfTxt, rows=1010:1024);
print(data);

unitName chromosome position NA06991,total NA06993,total NA07000,total
1010 SNP_A-2001589 1 34110291 954.6941 1022.368 1352.647
1011 SNP_A-2001596 1 34119149 4499.8872 4317.809 4380.319
1012 SNP_A-2001598 1 34119693 2138.8340 3229.630 2419.442
1013 SNP_A-2001642 1 34170728 5545.6758 6060.184 5707.734
1014 SNP_A-2001643 1 34172791 3561.7803 3469.545 3780.201
1015 SNP_A-4268291 1 34179429 2454.7314 1953.738 1925.875
1016 SNP_A-2001684 1 34204360 1435.8201 1353.817 1715.853
1017 SNP_A-4214101 1 34204556 3941.3589 3615.931 4174.944
1018 SNP_A-2001700 1 34211296 2232.3728 1784.901 2363.954
1019 SNP_A-2001835 1 34287073 3385.6470 2973.341 3188.489
1020 SNP_A-2001840 1 34306289 2451.4780 2415.758 3017.298
1021 SNP_A-4214120 1 34357252 3204.5381 2631.183 3220.736
1022 SNP_A-2001896 1 34377866 7543.6479 6363.690 6853.816
1023 SNP_A-4268333 1 34436399 1718.2601 1606.675 1876.243
1024 SNP_A-2002002 1 34519557 1620.9423 1946.391 1545.906

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