Question: cnv-seq in R language
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gravatar for sukesh1411
2.4 years ago by
sukesh141130
South Africa
sukesh141130 wrote:

Hi

I would like to identify the copy number variants in the plant genome. I am using CNV-seq to identify the cnvs. I tried to execute the cnv-seq.pl script to find cnvs using below command

./cnv-seq.pl --test my.hits --ref IRGSP-1.0_genome.fasta --log2-threshold=0.6 --genome rice --genome-size=373245519 -p 0.001 --bigger-window 2.

The minimum window size for detecting log2<=-0.6 should be 3376.08047608453 window size to use is 6018.00667741671 x 2 = 12036 window size to be used: 12036 read 37398153 test reads, out of 37398153 lines read 0 ref reads, out of 6220779 lines write read-counts into file: my.hits-vs-IRGSP-1.0_genome.fasta.log2-0.6.pvalue-0.001.count R package cnv output: my.hits-vs-IRGSP-1.0_genome.fasta.log2-0.6.pvalue-0.001.minw-4.cnv Error in library(cnv) : there is no package called ‘cnv’ Execution halted

But i could not load the library(cnv). Can anyone help me to load the cnv script in R. I installed cnvtools but its not the exact package it requires.

R • 1.6k views
ADD COMMENTlink written 2.4 years ago by sukesh141130

Did you follow the manual on their page about the installation? If you did are you sure it is correctly installed ? You should have the R package cnv installed in your computer to work? Do in a R terminal install.packages("cnv") or try it on bioconductor

ADD REPLYlink written 2.4 years ago by Lluís R.800

Thank you sir. I installed cnv package in R and its working now.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by sukesh141130
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