ChromoMap

Question

[pthom010]

I am trying to use the R package ChromoMap but I am not having any success. My input files look like this:

Chromosome Locations:

V1  V2  V3

1   SCA-6_Chr1  17110   42295411
2   SCA-6_Chr2  62  50830453
3   SCA-6_Chr3  2748    36683825
4   SCA-6_Chr4  88405   40508585
5   SCA-6_Chr5  3968    44910890
6   SCA-6_Chr6  42152   31248880
7   SCA-6_Chr7  107 29830994
8   SCA-6_Chr8  16007   22715421
9   SCA-6_Chr9  24  51217798
10  SCA-6_Chr10 3535    30185385

And my Gene List:

SCA-6_Chr1v1_00002  SCA-6_Chr1  21553   25466
SCA-6_Chr1v1_00006  SCA-6_Chr1  48967   53662
SCA-6_Chr1v1_00081  SCA-6_Chr1  421993  423489
SCA-6_Chr1v1_00094  SCA-6_Chr1  463254  465150
SCA-6_Chr1v1_00097  SCA-6_Chr1  470892  474295
SCA-6_Chr1v1_00162  SCA-6_Chr1  748619  750710
SCA-6_Chr1v1_00170  SCA-6_Chr1  794675  795169
SCA-6_Chr1v1_00188  SCA-6_Chr1  886541  887187
SCA-6_Chr1v1_00193  SCA-6_Chr1  909925  910239
SCA-6_Chr1v1_00249  SCA-6_Chr1  1190987 1196531

I keep getting the following error when I run this line of script:

ChromoMap(list(chromosome.locations, list(gene.list))

Error in pi[[j]] : subscript out of bounds

I have tried contacting the developer but I cannot reach them. Has anybody had luck with this package?

Answer 1

[lakshayanand15]

Hello,

In the R code that you shared, there is a syntactic error. The chromosome and annotation objects must be passed as lists separately. The correct syntax should be:

chromoMap( list(chromosome.locations) , list(gene.list) )

Please rectify your code and see if it produces the same error? Also, I am sorry that you weren’t able to reach me. I have been really busy with my PhD and other projects, but I always try my best to respond.

Thanks & Regards,

Lakshay