testDTU: Test function to obtain a top list of transcripts that are...

In jgilis/satuRn_jgilis: Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

Description

Function to test for differential transcript usage (DTU)

Usage

testDTU(object, contrasts, plot = FALSE, sort = FALSE)

Arguments

object	A 'SummarizedExperiment' instance containing a list of objects of the 'StatModel' class as obtained by the 'fitDTU' function of the 'satuRn' package.
contrasts	'numeric' matrix specifying one or more contrasts of the linear model coefficients to be tested. The rownames of the matrix should be equal to the names of parameters of the model that are involved in the contrast. The column names of the matrix will be used to construct names to store the results in the rowData of the SummarizedExperiment.
plot	'boolean(1)' Logical, defaults to FALSE. If set to TRUE, a plot of the histogram of the empirical z-scores and the standard normal distribution will bee displayed.
sort	'boolean(1)' Logical, defaults to FALSE. If set to TRUE, the output

Value

An updated 'SummarizedExperiment' that contains the 'Dataframes' displaying the significance of DTU for each transcript in each contrast of interest.

Author(s)

Jeroen Gilis

Examples

data(sumExp_example, package = "satuRn") # testDTU
sumExp <- fitDTU(
   object = sumExp_example,
   formula = ~0+group,
   parallel = FALSE,
   BPPARAM = BiocParallel::bpparam(),
   verbose = TRUE)
group <- as.factor(SummarizedExperiment::colData(sumExp)$group)
design <- model.matrix(~ 0 + group)
colnames(design) <- levels(group)
L <- matrix(0, ncol = 2, nrow = ncol(design))
rownames(L) <- colnames(design)
colnames(L) <- c("Contrast1", "Contrast2")
L[c("VISp.L5_IT_VISp_Hsd11b1_Endou", "ALM.L5_IT_ALM_Tnc"), 1] <- c(1, -1)
L[c("VISp.L5_IT_VISp_Hsd11b1_Endou", "ALM.L5_IT_ALM_Tmem163_Dmrtb1"), 2] <- c(1, -1)

sumExp <- testDTU(object = sumExp, contrasts = L, plot = FALSE, sort = FALSE)

jgilis/satuRn_jgilis documentation built on Jan. 21, 2021, 12:24 a.m.