A dataset containing gene expression of PTPRG in 60k microglia cells from the PsychAD Consortium from 299 subjects. Of these, 149 subjects have Alzheimer's disease, and 150 are neurotypical controls.
Usage
data(PsychAD)Format
A data frame with 60481 rows (i.e. cells) and 6 variables:
- SubID
subject identifer
- Sex
Sex
- Dx
Diagnosis: AD or Control
- Age
subject age
- PTPRG
number of RNA-seq counts for this gene
- libSize
total number of RNA-seq reads for this cell
Examples
data(PsychAD)
# model formula
form <- PTPRG ~ Dx + Age + Sex + offset(log(libSize)) + (1|SubID)
# fit negative binomial mixed model
fam <- negative.binomial(NA)
fit <- fastglmm(form, PsychAD, family=fam)
summary(fit)
#> Generalized linear mixed model fit by PQL ['fastglmm']
#> Family: Negative Binomial(0.2443) ( log )
#> Formula: PTPRG ~ Dx + Age + Sex + offset(log(libSize)) + (1 | SubID)
#>
#> Coefficients:
#> Estimate Std. Error df t value Pr(>|t|)
#> (Intercept) -8.577681 0.311172 149.9 -27.566 <2e-16 ***
#> DxAD 1.102755 0.073541 145.6 14.995 <2e-16 ***
#> Age -0.007262 0.003775 148.2 -1.923 0.0563 .
#> SexMale -0.103277 0.075756 145.7 -1.363 0.1749
#> ---
#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#>
#> Residual df: 60227.2
#>
#> Variance components:
#> sigSq_g: 0.4803
#> sigSq_e: 8.17
#> delta: 17.01
# Variance partitioning analysis
varpart(fit)
#> Dx Age Sex SubID CountNoise Residuals
#> 0.0133097371 0.0002197195 0.0001160483 0.0210313340 0.3062036641 0.6591194970