Methylkit (differential methylation analysis) error in data frame
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6 weeks ago
harshraje19 ▴ 40

Hi Friends, I am performing the differential methylation analysis using methylkit but it is throwing error in data frame. " Error in [.data.frame(data, , 6) : undefined columns selected". Can anyone help me to solve this error. Following is my R cmmand lnes. Thanks Raj

> library(methylKit)
> library(methylKit)
> file.list=list( "CpG_context_ST12_B1_F_bismark_hisat2_pe.txt","CpG_context_ST12_B2_F_bismark_hisat2_pe.txt","CpG_context_ST12_B3_F_bismark_hisat2_pe.txt","CpG_context_ST2_B1_F_bismark_hisat2_pe.txt","CpG_context_ST2_B2_F_bismark_hisat2_pe.txt","CpG_context_ST2_B3_F_bismark_hisat2_pe.txt")
> 
> myobj=methRead(file.list,
+                  sample.id=list("test1","test2","test3","ctrl1","ctrl2","ctrl3"),
+                  assembly="Edwards",
+                  treatment=c(1,1,1,0,0,0),
+                  context="CpG",
+                  mincov = 10,
+                  pipeline = "bismark"
+   )
Received list of locations.
Reading file.
|--------------------------------------------------|
|==================================================|
Error in `[.data.frame`(data, , 6) : undefined columns selected
methylation differential analysis R methylkit • 426 views
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Maybe your file format is not the adequate for the import of the files by methylKit with the method pipeline = "bismark" ? It says in the methRead documentation that it expects a tabular format as shown in the github:

chrBase chr base    strand  coverage    freqC   freqT
chr21.9764539   chr21   9764539 R   12  25.00   75.00
chr21.9764513   chr21   9764513 R   12  0.00    100.00

Are the files you're imputting in that format? If not, you may input Bismark coverage or cytosine report files using the other pipeline options available in the function

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Hi. Thank you for your response.

My file look like this. Do you think it is wrong format?

(base) harshraj@harshraj-XPS-8930:~/Desktop/DMR$ head -10 CpG_context_ST12_B1_F_bismark_hisat2_pe.txt 
Bismark methylation extractor version v0.23.0
A00821:696:H77L5DSX2:1:1101:12454:1016_1:N:0:TATAGCGG+GAACTGAC  -   7   336731  z
A00821:696:H77L5DSX2:1:1101:12454:1016_1:N:0:TATAGCGG+GAACTGAC  -   7   336941  z
A00821:696:H77L5DSX2:1:1101:12454:1016_1:N:0:TATAGCGG+GAACTGAC  -   7   336883  z
A00821:696:H77L5DSX2:1:1101:13774:1016_1:N:0:TATAGCGG+GAACTGAC  +   14  2476108 Z
A00821:696:H77L5DSX2:1:1101:19759:1016_1:N:0:TATAGCGG+GAACTGAC  +   7   1367984 Z
A00821:696:H77L5DSX2:1:1101:25699:1031_1:N:0:TATAGCGG+GAACTGAC  +   6   6834064 Z
A00821:696:H77L5DSX2:1:1101:25699:1031_1:N:0:TATAGCGG+GAACTGAC  +   6   6834057 Z
A00821:696:H77L5DSX2:1:1101:25699:1031_1:N:0:TATAGCGG+GAACTGAC  -   6   6833845 z
A00821:696:H77L5DSX2:1:1101:18240:1047_1:N:0:TATAGCGG+GAACTGAC  -   9   9152550 z
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Hmm no it does not look like the same format. As I said, I would suggest imputing either Bismark coverage or cytosine report files and using pipeline = "bismarkCoverage" or "bismarkCytosineReport". You can recognize the files from Bismark by doing head and checking with the Bismark manual.

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]Can i use these files, enter image description here

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Use either those ending in "bismark.cov.gz" or "CpG_report.txt.gz" with pipeline = "bismarkCoverage"orpipeline = "bismarkCytosineReport", respectively.

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It worked i used "bismark.cov.gz" file with pipeline = "bismarkCoverage". Thank you so much, i was struggling with this for week

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