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

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

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: 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\>[email protected]\</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