Error: line 1 did not have 7 elements. --Putting bismark extractor files into methimpute
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Entering edit mode
8 weeks ago
sam • 0
file <- system.file("extdata","file.txt", package="methimpute")
data(arabidopsis_chromosomes)
arabidopsis_chromosomes$chromosome <- sub('chr', '', arabidopsis_chromosomes$chromosome)
bismark.data <- importBismark(file, chrom.lengths=arabidopsis_chromosomes)

I am trying to interpret my bismark results into methimpute but it gives me an error of :

line 1 did not have 7 elements
In addition: Warning messages:
1: In data.table::fread(file, skip = skip, sep = "\t", colClasses = classes) :
  Detected 7 column names but the data has 2 columns. Filling rows automatically. Set fill=TRUE explicitly to avoid this warning.
2: In utils::read.table(file, skip = skip, sep = "\t", colClasses = classes) :
  line 1 appears to contain embedded nulls

The problem is I don't know which type of BÄ°smark file I need to provide for this. Thank you for your time already.

RNA-seq • 180 views
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Entering edit mode

The problem is linked to file reading in R. Probably your file is badly formatted.

You should read carefully the error message:

Detected 7 column names but the data has 2 columns

You have 7 names and 2 columns. Maybe bismark expects 7 columns?

If you post the first lines (including header) of your file, maybe someone could help.

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