Error in RCircos.Validate.Genomic.Data:One or more genomic position in plot data is outside of chromosome length for Mchr5.
0
1
Entering edit mode
5.8 years ago
user_g ▴ 20

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 • 1.5k views
ADD COMMENT

Login before adding your answer.

Traffic: 4037 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6