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

Write annotation data as a tab-delimited text file

Author: Henrik Bengtsson
Created on: 2010-04-27

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.

See also

To write non-annotation data, see how-to page 'Write data as a tab-delimited text file'.

Example: Exporting an UGP file to a tab-delimited text file

library("aroma.core");

ugp <- AromaUgpFile$byChipType("Mapping10K_Xba142");
print(ugp);

AromaUgpFile:
Name: Mapping10K_Xba142
Tags: na26,HB20080916
Full name: Mapping10K_Xba142,na26,HB20080916
Pathname: ../../../Documents/My Data/annotationData/chipTypes/Mapping10K_Xba142/
Mapping10K_Xba142,na26,HB20080916.ugp
File size: 50.45 kB (51663 bytes)
RAM: 0.00 MB
Number of data rows: 10208
File format: v1
Dimensions: 10208x2
Column classes: integer, integer
Number of bytes per column: 1, 4
Footer: <createdOn>20080916 18:46:43 PDT</createdOn><platform>Affymetrix</platfo
rm><chipType>Mapping10K_Xba142</chipType><createdBy><fullname>Henrik Bengtsson</
fullname><email>hb@stat.berkeley.edu</email></createdBy><srcFiles><srcFile1><fil
ename>Mapping10K_Xba142.cdf</filename><filesize>9995717</filesize><checksum>ad6e
f2568ad7c629c4218b3f402a5cf4</checksum></srcFile1><srcFile2><filename>Mapping10K
_Xba142.na26.annot.csv</filename><filesize>16140044</filesize><checksum>666197b5
7c567684d370cfa8e68057d2</checksum></srcFile2></srcFiles>
Chip type: Mapping10K_Xba142
Platform: Affymetrix

AromaUgpFile:Name: Mapping10K_Xba142
Tags: na26,HB20080916
Full name: Mapping10K_Xba142,na26,HB20080916
Pathname: annotationData/chipTypes/Mapping10K_Xba142/Mapping10K_Xba142,na26,HB20080916.ugp
File size: 50.45 kB (51663 bytes)
RAM: 0.00 MB
Number of data rows: 10208
File format: v1
Dimensions: 10208x2
Column classes: integer, integer
Number of bytes per column: 1, 4
Footer: <createdOn>20080916 18:46:43 PDT</createdOn><platform>Affymetrix</platform><chipType>Mapping10K_Xba142</chipType>
<createdBy><fullname>Henrik Bengtsson</fullname><email>hb@stat.berkeley.edu</email></createdBy>
<srcFiles><srcFile1><filename>Mapping10K_Xba142.cdf</filename><filesize>9995717</filesize>
<checksum>ad6ef2568ad7c629c4218b3f402a5cf4</checksum></srcFile1>
<srcFile2><filename>Mapping10K_Xba142.na26.annot.csv</filename><filesize>16140044</filesize>
<checksum>666197b57c567684d370cfa8e68057d2</checksum></srcFile2></srcFiles>
Chip type: Mapping10K_Xba142
Platform: Affymetrix

ugpTxt <- writeDataFrame(ugp, columnNamesPrefix="none");
print(ugpTxt);

TabularTextFile:
Name: Mapping10K_Xba142
Tags: na26,HB20080916.ugp
Full name: Mapping10K_Xba142,na26,HB20080916.ugp
Pathname: annotationData/chipTypes/Mapping10K_Xba142/Mapping10K_Xba142,na26,HB20080916.ugp.txt
File size: 265.78 kB (272154 bytes)
RAM: 0.01 MB
Number of data rows: 10220
Columns [3]: 'unitName', 'chromosome', 'position'
Number of text lines: 10221

data <- readDataFrame(ugpTxt, rows=1:10);
print(data);

        unitName chromosome  position
1    AFFX-5Q-123         NA        NA
2    AFFX-5Q-456         NA        NA
3    AFFX-5Q-789         NA        NA
4    AFFX-5Q-ABC         NA        NA
5  SNP_A-1513509          6 162491313
6  SNP_A-1518411          7  42608794
7  SNP_A-1511066         10  68113302
8  SNP_A-1517367          1  22754354
9  SNP_A-1512567         15  28848178
10 SNP_A-1519604         12  53641300