Question: Print Differentially Expressed Exons From Dexseq Results
1
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3 months ago
justinkablan225 • 10

Hello, I'm trying to do some differential expressed exons analysis with DEXSeq package. I got DEXSeq results by :

dxr1 = DEXSeqResults( dxdEFC, padj>=0.1 )

Then, I'm looking for print only Up-regulate or Down-regulate exons significantly expressed.

Therefore, I done :

write.table(dxr1, "DEXSeq_results" , sep="\t", col.names=T, row.names = T)

This script gave me all genes and exons in a single file within more than 60.000 rows what is very difficult to open and then difficult to sort by padj or FDR.

I think that someone can help me here to resolve that, I will be very grateful.

Best regards.

ADD COMMENTlink 3 months ago justinkablan225 • 10
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0

Dear all,

You don't know how you save me. May GOD bless you more and more.

ADD REPLYlink 3 months ago
justinkablan225
• 10 • updated 3 months ago
lieven.sterck
5.1k
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0

Hello,

After printing result, I see that some same genes names are listed again in the table with another exonID. Then I've too much genes and exons, that I want is to group same geneID in one wich would group all his exons.

ADD REPLYlink 3 months ago
justinkablan225
• 10 • updated 3 months ago
lieven.sterck
5.1k
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0

Did you mean something like the following?

  groupID     featureID_by_groupID         
1 FBgn0000256 E009,E010,E013      
2 FBgn0000578 E009                
3 FBgn0002921 E012,E015           
4 FBgn0010909 E010                
5 FBgn0020309 E007                
6 FBgn0027579 E001,E002
ADD REPLYlink 3 months ago
SMK
♦ 1.3k
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Yes, exactly that.

ADD REPLYlink 3 months ago
justinkablan225
• 10 • updated 3 months ago
lieven.sterck
5.1k
Entering edit mode
1

It can be generated by:

dxr1.sig <- as.data.frame(dxr1[dxr1$padj < 0.1 & !is.na(dxr1$padj),])
library(dplyr)
dxr1.sig.genes <- dxr1.sig %>%
  select(groupID, featureID) %>%
  group_by(groupID) %>%
  mutate(featureID_by_groupID = paste(featureID, collapse = ",")) %>%
  select(-featureID) %>%
  unique()
ADD REPLYlink 3 months ago
SMK
♦ 1.3k
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Hello Thanks lot. It's work perfectly.

ADD REPLYlink 3 months ago
justinkablan225
• 10
2
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3 months ago
SMK ♦ 1.3k
Ghent, Belgium

Try:

dxr1.sig <- as.data.frame(dxr1[dxr1$padj < 0.1 & !is.na(dxr1$padj),])

then save dxr1.sig using your write.table.

ADD COMMENTlink 3 months ago SMK ♦ 1.3k
2
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3 months ago
lieven.sterck 5.1k
VIB, Ghent, Belgium

since you have gotten to the point where you have tab-delineated file with your values, use linux sort or even better awk. Those are applications that allow for easy and powerful manipulation (sorting, filtering on values, ... ) of tab files.

ADD COMMENTlink 3 months ago lieven.sterck 5.1k

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