how to normalize GC content using cqn function
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Entering edit mode
3.4 years ago
pt.taklifi ▴ 60

Hello everyone . I have a count matrix of sequencing data showing how many fragments there is in each region here is a few rows of my data

head(data[,1:6])
 [,1] [,2] [,3] [,4] [,5] [,6]
1    3    6    0    0    3    1
2    4    4    0    0    0    0
3    4    4    1    0    2    2
4    0    2    0    0    0    0
5    0    1    0    0    0    0
6    0    5    2    0    0    0

I am trying to GC content normalize my data first I did a quantile normalization with normalize.quantiles function and named output data.norm. then I calculated GC content for each region .Finally using cqn i tried to do GC content normalization

cqn( data.norm, x=gc ,lengths = l)

but I get the following error

 Error in qr.default(t(const)) : 
      NA/NaN/Inf in foreign function call (arg 1)

I'm not familiar with cqn package so I don't exactly know what is the problem here

cqn software error • 952 views
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