Search found 3 matches

by biancaneve
Fri Feb 10, 2017 10:21 am
Forum: GenABEL
Topic: use grammar-gamma or grammar-gc
Replies: 0
Views: 1255

use grammar-gamma or grammar-gc

I wonder whether to use grammar “gamma” or grammar “gc”. I still do not understand the difference between them. As suggested by the Package ‘GenABEL’ (February 19, 2015) , I read the papers by Amin N, van Duijn CM, Aulchenko YS. PLoS ONE (for GRAMMAR-GC) and Svischeva G, Axenovich TI, Belonogova NM,...
by biancaneve
Fri Jan 20, 2017 8:58 am
Forum: GenABEL
Topic: variance explained by each SNP
Replies: 0
Views: 1346

variance explained by each SNP

I am using the GenABEL package and I have 900 cows genotyped at the HD Illumina SNP panel. 630 thousand markers passed the quality check. The analyzed phenotype is longevity expressed in days from first calving to culling, mean=1578 ± 665 days. For each marker I have: 1. Effect of the minor allele 2...
by biancaneve
Fri Sep 30, 2016 12:53 pm
Forum: GenABEL
Topic: h2 values to use in the instruction: a <-grammar(h2ht,data=df)
Replies: 0
Views: 1515

h2 values to use in the instruction: a <-grammar(h2ht,data=df)

I must calculate heritability of two traits (tr1 and tr2) in order to perform association analysis with Bovine Illumina BeadChip (777,962 markers) using the following function: a_tr <-grammar (h2ht, data=data868) I have 900 individuals, two fixed effects: farm and year of birth, the traits are the f...

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