Question: Error in RCircos.Validate.Genomic.Data:One or more genomic position in plot data is outside of chromosome length for Mchr5.
1
gravatar for user_g
2.3 years ago by
user_g20
user_g20 wrote:

Hello, I have the following data which I want to plot on Rcircus and link them.

 srcTName srcTStart srcTEnd SeqNames    Start      End
1   Hchr18    657287  658525    Mchr5 30072897 30073562
2   Hchr18    830267  830721    Mchr5 32594399 32594708
3   Hchr18    903627  905104   Mchr17 93198252 93199733
4   Hchr18   2571338 2571954   Mchr17 71526682 71527049
5   Hchr18   2654877 2655933   Mchr17 71475296 71476291
6   Hchr18   2654877 2655933    Mchr1 18058862 18059032

The H represents Human chromosome, while M represents Mouse chromosome. I want to draw the link between the elements of each row, for example link between Hchr18 657287 to Mchr5 30072897.

I always get this error:

 Error in RCircos.Validate.Genomic.Data(genomic.data, "link",
 genomic.columns) :    One or more genomic position in plot data is
 outside of chromosome length for Mchr5.

I got the mapped coordinates using pslMap, I also checked the coordinates manually and they are fine so I do not know why I am getting this error.

R rcircus • 585 views
ADD COMMENTlink modified 2.3 years ago by RamRS30k • written 2.3 years ago by user_g20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 889 users visited in the last hour