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Add qvalue columns to the glmmSeq dataframe

Usage

glmmQvals(object, cutoff = 0.05, verbose = TRUE)

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