glmmQvals {glmmSeq}

Glmm Sequencing qvalues

Description

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)