format of lower triangle elements of the GRM to binary files

OXTR11
Guest

format of lower triangle elements of the GRM to binary files Jan 20, 2015 10:42:09 GMT

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Post by OXTR11 on Jan 20, 2015 10:42:09 GMT

I just have problems of interpreting the GRM files after processing the binaries with the R script on the GCTA page. How can I reconstruct the triangle elements, so that I know
the relationship coefficient between each pair of individuals? What is the meaning of the columns.
Thank you very much in advance
Best
Martin

Zhihong Zhu
Moderator

Posts: 88

format of lower triangle elements of the GRM to binary files Jan 22, 2015 3:03:16 GMT

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Post by Zhihong Zhu on Jan 22, 2015 3:03:16 GMT

Hi Martin,

The meaning of each column can be found at www.complextraitgenomics.com/software/gcta/estimate_grm.html, which are respectively index of individual 1 (row number of a sample id), index of individual 2, number of non-missing SNPs, estimate of genetic relatedness.

If you're going to update the GRM file, a possible way is to generate the GRM as .gz format, and modify the last column.

Cheers,
Zhihong

OXTR11 Guest	format of lower triangle elements of the GRM to binary files Jan 22, 2015 18:35:13 GMT Quote Select Post Deselect Post Link to Post Back to Top Post by OXTR11 on Jan 22, 2015 18:35:13 GMT Dear Zhihong, Thanks a lot! Best Martin

OXTR11 Guest	format of lower triangle elements of the GRM to binary files Jan 22, 2015 18:36:24 GMT Quote Select Post Deselect Post Link to Post Back to Top Post by OXTR11 on Jan 22, 2015 18:36:24 GMT Dear Zhihong, Thanks a lot! Best Martin

format of lower triangle elements of the GRM to binary files

Post by OXTR11 on Jan 20, 2015 10:42:09 GMT

Post by Zhihong Zhu on Jan 22, 2015 3:03:16 GMT

Post by OXTR11 on Jan 22, 2015 18:35:13 GMT

Post by OXTR11 on Jan 22, 2015 18:36:24 GMT