Add qvalue columns to the glmmSeq dataframe
Arguments
- object
A glmmSeq/lmmSeq object created by
glmmSeq::glmmSeq().- cutoff
Prints a table showing the number of probes considered significant by the pvalue cut-off (default=0.05)
- verbose
Logical whether to print the number of significant probes (default=TRUE)
Value
Returns a GlmmSeq object with results for gene-wise general linear mixed models with adjusted p-values using the qvalue function
Examples
data(PEAC_minimal_load)
disp <- apply(tpm, 1, function(x) {
(var(x, na.rm=TRUE)-mean(x, na.rm = TRUE))/(mean(x, na.rm = TRUE)**2)
})
MS4A1glmm <- glmmSeq(~ Timepoint * EULAR_6m + (1 | PATID),
countdata = tpm[1:5, ],
metadata = metadata,
dispersion = disp[1:5],
verbose=FALSE)
MS4A1glmm <- glmmQvals(MS4A1glmm)
#>
#> Timepoint
#> ---------
#> Not Significant Significant
#> 2 3
#>
#> EULAR_6m
#> --------
#> Not Significant Significant
#> 3 2
#>
#> Timepoint:EULAR_6m
#> ------------------
#> Not Significant
#> 5