FourCSeq problem with getZScores and multiple viewpoints
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dzis • 0
@dzis-8446
Last seen 5.7 years ago
Poland

Hi,

I am using FourCseq with one 4C experiment with 2 biological replicates and 2 view points.:

DataFrame with 4 rows and 5 columns
    viewpoint condition replicate              bamFile sequencingPrimer
  <character>  <factor> <numeric>          <character>      <character>
1        FLC1         A         1 INDEX_1_3.sorted.bam            first
2        FLC1         A         2 INDEX_1_4.sorted.bam            first
3        FLC2         B         1 INDEX_1_5.sorted.bam            first
4        FLC2         B         2 INDEX_1_6.sorted.bam            first

 

When I run:

fcf <- getZScores(fc)

I get the following error:

Error in getZScores(fc) :
  None or more than one viewpoint are contained in the 'FourC' object.
         Use a 'FourC' object that contains only one viewpoint.

The pipeline doesnt support multiple view points?

Could you please help me with this if it is possible to run it with 2 viewpoints ?

Best Regards

Dimitris

 

FourCSeq getZScores viewpoints software error • 660 views
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Entering edit mode
dzis • 0
@dzis-8446
Last seen 5.7 years ago
Poland

I think that i found the solution which is :

 

fcf1 <- getZScores(fc[,c("FLC1_A_1", "FLC1_A_2")])
fcf2 <- getZScores(fc[,c("FLC2_B_1", "FLC2_B_2")])

i had to select each viewpoint with his replicates in order to have the Zscorres. Thanks for the inspiration !

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