How do I extract data from a .ab1 file ?
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anuragm • 0
@anuragm-7148
Last seen 6.4 years ago
India

I am trying to extract information about the nucleotide signal strength at each location for a .ab1 file. Basically I want the ratio of the parameters P1AM and P2AM

library(sangerseqR)
x=read.abif(file.choose())
x$P1AM

This gives me an error saying $ is not an operator for Class S4. Is there a way to achieve what I am trying to do ?

 

 

ab1 sequence sangerseqR • 882 views
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@aaronlstatham-6743
Last seen 6.2 years ago
Australia

The 'P1AM' and 'P2AM' fields are inside the 'Data' slot - you can find this by using str(x). You can pull out these fields using the @ operator - x@Data$P1AM will do the trick.

 

 

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I am getting output NULL. What could be wrong ?

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