GTEx reaction rates h2 similar to permuted h2

Haky Im

2020-11-02

We want to investigate whether reaction rates estimated with imat(?) are heritable. Reaction rates (binary variables) were estimated by D using GTEx gene expression data.

Initially, D generated reaction rates with brain cortex expression data from ~250 individuals.

Heritability of reaction rates was calculated with GCTA. Actual observed h2 and two permuted h2 values are compared next. Spoiler alert: no difference between actual and permuted values. :(

tempo = read_tsv(glue::glue("{DATA}/df.GTEX.txt"))
## Parsed with column specification:
## cols(
##   Phenotype = col_double(),
##   H2 = col_double(),
##   Perm1 = col_double(),
##   Perm2 = col_double(),
##   `H2 constrained` = col_double(),
##   `Perm constrained 1` = col_double(),
##   `Perm Constrained 2` = col_double()
## )
tempo_constrained = tempo %>% select(pheno=Phenotype,observed=`H2 constrained`, perm1=`Perm constrained 1`, perm2=`Perm Constrained 2`) 
tempo_constrained %>% pivot_longer(-pheno, names_to = "type", values_to="h2") %>% ggplot(aes(h2)) + geom_histogram() + facet_wrap(~type)
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

qqplots comparing actual vs permuted h2

qqplot(tempo_constrained$observed, tempo_constrained$perm1); abline(0,1)

qqplot(tempo_constrained$observed, tempo_constrained$perm2); abline(0,1)

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Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The source code is licensed under MIT.

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Citation

For attribution, please cite this work as

Haky Im (2020). GTEx reaction rates h2 similar to permuted h2. ImLab Notes. /post/2020/11/02/testing-personal-notebook/

BibTeX citation

@misc{
  title = "GTEx reaction rates h2 similar to permuted h2",
  author = "Haky Im",
  year = "2020",
  journal = "ImLab Notes",
  note = "/post/2020/11/02/testing-personal-notebook/"
}