MAnorm error in script

Question

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I am using MAnorm for differential peak analysis and while running MAnorm.r I am getting following Error:

Ops.data.frame((common_peak_count_read1 + 1), (common_peak_count_read2 + : ‘/’ only defined for equally-sized data frames Execution halted

when I looked into the source code the error is output of following command :

M<-log2((common_peak_count_read1+1)/(common_peak_count_read2+1))

I am not sure what is meant by equally-sized data frames here? Any suggestions on this ?

[Ram]

This is an R script, not a shell script. Your code looks like a custom function, but the error could mean that the custom function can only operate on data frames that have an equal number of rows and columns. You're going to have to dig deeper to find why your input does not generate those equally sized data frames.

Answer 1

[Moshe Roseman]

Hi,

I got the same error. It appears to be due to a change in bedtools coverage from May 2015 (see the note marked "important" in the bedtools coverage page: http://bedtools.readthedocs.io/en/latest/content/tools/coverage.html)

To fix this, you should edit the MAnorm.sh code, look for all the lines beginning with "coverageBed" and replace one input file with the other.

For example:

coverageBed -a read1.bed -b unique_peak1.bed

should be changed to:

coverageBed -b read1.bed -a unique_peak1.bed

Good luck!