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?
•
written
by
pthom010 •
1 answer
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
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