User: daijieqiong

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daijieqiong10
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Posts by daijieqiong

<prev • 7 results • page 1 of 1 • next >
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Answer: A: Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TR
...   Hi Günter, it shows that: > bamDataRanges1 <- getReadCountsFromBAM("/data/daij/project/CNV/new/SCD151-3.bam",refSeqName=c("chr1","chr2", "chr3", "chr4", "chr5","chr6", "chr7", "chr8","chr9","chr1Identified the following reference sequences:  HPV16_Ref,chr1,chr2,chr3,chr4,chr5,chr6,chr7,ch ...
written 22 months ago by daijieqiong10
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Answer: A: Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TR
... Hi Günter, I did some test with the bam file that can not be processed by getReadCountsFromBAM. I found that when I run it with each chromosome one by one, it is fine. But when I run it with all the chromosome at the same time, it shows "Error in if (sum(rds.counts) == 0) { : missing value where TR ...
written 22 months ago by daijieqiong10
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Comment: C: GenVisR- cnSpec CNV plot
... Hi Zach, One more question. I am trying to use coord_flip() to flip over the x and y axis, but seems the axis tick marks cannot be flipped.  Could you please show me the right way to do that? Thanks again for your great helps! Jieqiong ...
written 22 months ago by daijieqiong10
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Answer: A: GenVisR- cnSpec CNV plot
... Hi Zach, Thanks very much for your great help. As you suggested , I will add a padding to the start and stop in the actual data to make it more visible. By the way, which color code will you suggest to replace the default red for a better vision? I have tried to play with several different colors ...
written 22 months ago by daijieqiong10
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GenVisR- cnSpec CNV plot
... Dear Dr Skidmore, I am using GenVisR to plotting my CNV result and found it very helpful. Here I have two question regarding the cnSpec function, and could you please help me to figure them out? 1. how to adjust the thickness of the CNV lines within each chromosome to make them more visible? I tr ...
genvisr written 22 months ago by daijieqiong10
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Answer: A: Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TR
... Hi Günter, Thanks very much for you reply. yes, I found one of my bam files has some issue to cause the problem after checking them one by one. Problem has solved after removing that sample.   Jieqiong   ...
written 22 months ago by daijieqiong10
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Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
... Dear Dr Klambauer, I met a problem when using cn.mops for CNV analysis for my WGS samples. It worked fine when I did the test run with two samples. However, when I run more than 10 samples, the error message comes out at the first bam file reading procedure. > library(cn.mops) > ...
cn.mops software error written 22 months ago by daijieqiong10

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