Plotting the control-FREEC data

Question

[sainavyav22]

I used the control-FREEC for copy number aberration analysis of whole genome sequenced DNA of dog genome. I tried to plot the data with makeGraph2.0.R script in control-FREEC. But it plotted only chromosomes from 26 to 38. I received a warning message as well. Could some please help how to resolve this issue. Thanks. Warning message: INFO: Selected ploidy: 2 null device 1 Warning messages: 1: In xy.coords(x, y, xlabel, ylabel, log) : NaNs produced 2: In xy.coords(x, y, xlabel, ylabel, log) : NaNs produced 3: In xy.coords(x, y, xlabel, ylabel, log) : NaNs produced 4: In xy.coords(x, y, xlabel, ylabel, log) : NaNs produced 5: In xy.coords(x, y, xlabel, ylabel, log) : NaNs produced 6: In xy.coords(x, y, xlabel, ylabel, log) : NaNs produced 7: In xy.coords(x, y, xlabel, ylabel, log) : NaNs produced 8: In xy.coords(x, y, xlabel, ylabel, log) : NaNs produced

cat makeGraph2.0.R | R --slave --args ChestercfDNA_NEW_alignment_sorted.bam_ratio.txt

Answer 1

[RD]

Did you modify the Chr list in makeGraph2.0.R with dog Chr names.