Extracting specific data from the grm.bin

bb
New Member

Posts: 3

Extracting specific data from the grm.bin Sept 29, 2016 8:19:12 GMT

Quote

Post by bb on Sept 29, 2016 8:19:12 GMT

Dear All

I have a problem regarding the grm.bin. I have built a large (100k individuals) grm in binary format. Now I want to extract specific relationships according to a given list (combinations of individuals) (1) and I want to extract relationships higher than a predefine threshold (2). The keep/remove options do not fit my requirements and the provided R-Script is not fast enough.
The easiest way for me seems to read the grm.bin with a C++ program because I have written my downstream programs also in C++.

Does anyone of you have experiences with reading the grm.bin with a C++ function or could even anyone of you provide a C++ function to read the grm.bin to extract specific data in ascii format?

I am very glad about all hints or efforts.

Thanks a lot and best regards

Beat

Zhihong Zhu
Moderator

Posts: 88

Extracting specific data from the grm.bin Sept 30, 2016 7:40:31 GMT

Quote

Post by Zhihong Zhu on Sept 30, 2016 7:40:31 GMT

Hi Beat,

In my opinion, there are two solutions,

1. try '--grm-cutoff' to know what those individuals having higher relationship than your threshold are. Then probably you could keep those individuals in a new GRM (.gz format)
2. GCTA source code must have C++ code to read GRM, trying searching '--grm'.

Cheers,
Zhihong

bb New Member Posts: 3	Extracting specific data from the grm.bin Oct 12, 2016 14:08:55 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by bb on Oct 12, 2016 14:08:55 GMT Hi Zhihong Thanks a lot for providing the two solutions. Concerning the second one I do not understand what you mean exactly: Deriving from GCTA source code reading routines for grm.bin? Thanks and regards Beat

bb New Member Posts: 3	Extracting specific data from the grm.bin Oct 12, 2016 14:09:20 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by bb on Oct 12, 2016 14:09:20 GMT Hi Zhihong Thanks a lot for providing the two solutions. Concerning the second one I do not understand what you mean exactly: Deriving from GCTA source code reading routines for grm.bin? Thanks and regards Beat

Zhihong Zhu Moderator Posts: 88	Extracting specific data from the grm.bin Oct 13, 2016 23:14:49 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by Zhihong Zhu on Oct 13, 2016 23:14:49 GMT Hi Beat, Yes, if you are interested in how GCTA reads the GRM file. But the first one would be easier. Cheers, Zhihong

Post by bb on Sept 29, 2016 8:19:12 GMT

Post by Zhihong Zhu on Sept 30, 2016 7:40:31 GMT

Post by bb on Oct 12, 2016 14:08:55 GMT

Post by bb on Oct 12, 2016 14:09:20 GMT

Post by Zhihong Zhu on Oct 13, 2016 23:14:49 GMT