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tpbilton / GUSMap

Genotyping Uncertainty with Sequencing data and linkage MAPping
GNU General Public License v3.0
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Criteria for analysis-in-gusmap #5

Closed ke-shi closed 5 years ago

ke-shi commented 6 years ago

I finished "Reading Data into GUSMap:" part safely, and tried the next "Analysis in GUSMap:". The description for this step is difficult for me to understand... Why did you set the following SNPs as TRUE?:

badSnps[c(3:14,16,18:23,25:27,29,33:35,39:42,44,46:49, 53,58:60,63,65:67,69:74,76,77,85,104,114:129, 152,162,163,173:180,187:190,206:208,210,212,213, 216,228,272,285,286,298,304,314,318,320,342,344,345, 354,358,370,373,380,389,390,397,408,411,421,427, 437,446,469,493,498:500,506,510,516,519,522,531, 543,553,556,569,582,585,601,617,620,623,628,635, 636:643,647:650,669:680)] <- TRUE

Thanks, Kenta

tpbilton commented 6 years ago

Hi Kenta,

The reason for why these SNPs where discarded was that they appeared to be mis-ordered or located on a different chromosome based on a heatmap of the two-point recombination fractions. (see Figure S11 in supplementary file File S2 in the publication that goes with the package).

I'd admit that the example may not be all that clear. The analysis in the example was done to replicate the analysis in the paper somewhat.

Timothy P.S. I'm intending to do some modifications to the package that include further functionality (such as computing the 2-point rf estimates and ordering etc). However, if you would like some code for computing the 2-point estimates now, let me know and I post it.