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Forum: Bioinformatics 08-11-2014, 11:33 PM
Replies: 13
Views: 5,623
Posted By xiechao
Thank you very much for the bugfix. The files are...

Thank you very much for the bugfix. The files are updated.
Forum: Bioinformatics 08-06-2014, 12:51 AM
Replies: 6
Views: 2,030
Posted By xiechao
The "cnv" column is the CNV region ID (0 means...

The "cnv" column is the CNV region ID (0 means that window is not part of any CNV).
Forum: Bioinformatics 08-06-2014, 12:50 AM
Replies: 6
Views: 2,030
Posted By xiechao
Yes, positive log2 means more copies in "test"...

Yes, positive log2 means more copies in "test" than "ref".
Forum: Bioinformatics 08-06-2014, 12:46 AM
Replies: 2
Views: 1,387
Posted By xiechao
Each row describes one sliding window position,...

Each row describes one sliding window position, so the columns "p.value" and "log2" are for that window. Then there is a column called "cnv", which is saying whether that window is part of a CNV...
Forum: Literature Watch 07-16-2014, 07:58 PM
Replies: 46
Views: 44,270
Posted By xiechao
Try something like: g <- plot.cnv(data, CNV =...

Try something like:
g <- plot.cnv(data, CNV = 4)
g + theme(axis.text.x = element_text(angle = 90))
Forum: Literature Watch 07-16-2014, 06:47 PM
Replies: 46
Views: 44,270
Posted By xiechao
Yes, it should work with any genome. But you need...

Yes, it should work with any genome. But you need to specify --genome-size, which is used for sliding window size calculation.
Forum: Bioinformatics 07-09-2014, 08:08 PM
Replies: 13
Views: 5,623
Posted By xiechao
The last 3 columns are referring to CNV_Region,...

The last 3 columns are referring to CNV_Region, so if a sliding window is not part of a CNV region, the values will be NA.
If all values for the 3 columns are NA, it means no CNV region was found...
Forum: Literature Watch 03-25-2009, 02:22 AM
Replies: 46
Views: 44,270
Posted By xiechao
CNV-seq, to detect Copy Number Variation using next-generation sequencing

CNV-seq, a new method to detect copy number variation using high-throughput sequencing.

more details at BMC Bioinformatics :
http://www.biomedcentral.com/1471-2105/10/80

The package is at...
Forum: Bioinformatics 03-23-2009, 12:57 AM
Replies: 236
Views: 654,360
Posted By xiechao
CNV-seq

a package to detect DNA copy number variation using shotgun sequencing.
http://tiger.dbs.nus.edu.sg/cnv-seq/
http://www.biomedcentral.com/1471-2105/10/80
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