dmTest: Likelihood ratio test to detect differential transcript/exon...
In DRIMSeq: Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

Description Usage Arguments Details Value Author(s) References See Also Examples

First, estimate the null Dirichlet-multinomial and beta-binomial model parameters and likelihoods using the null model design. Second, perform the gene-level (DM model) and feature-level (BB model) likelihood ratio tests. In the differential exon/transcript usage analysis, the null model is defined by the null design matrix. In the exon/transcript usage QTL analysis, null models are defined by a design with intercept only. Currently, beta-binomial model is implemented only in the differential usage analysis.

dmTest(x, ...)

## S4 method for signature 'dmDSfit'
dmTest(x, coef = NULL, design = NULL, contrast = NULL,
  one_way = TRUE, bb_model = TRUE, prop_mode = "constrOptim",
  prop_tol = 1e-12, coef_mode = "optim", coef_tol = 1e-12, verbose = 0,
  BPPARAM = BiocParallel::SerialParam())

## S4 method for signature 'dmSQTLfit'
dmTest(x, permutation_mode = "all_genes",
  one_way = TRUE, prop_mode = "constrOptim", prop_tol = 1e-12,
  coef_mode = "optim", coef_tol = 1e-12, verbose = 0,
  BPPARAM = BiocParallel::SerialParam())

`x`	`dmDSfit` or `dmSQTLfit` object.
`...`	Other parameters that can be defined by methods using this generic.
`coef`	Integer or character vector indicating which coefficients of the linear model are to be tested equal to zero. Values must indicate column numbers or column names of the `design` used in `dmFit`.
`design`	Numeric matrix defining the null model.
`contrast`	Numeric vector or matrix specifying one or more contrasts of the linear model coefficients to be tested equal to zero. For a matrix, number of rows (for a vector, its length) must equal to the number of columns of `design` used in `dmFit`.
`one_way`	Logical. Should the shortcut fitting be used when the design corresponds to multiple group comparison. This is a similar approach as in `edgeR`. If `TRUE` (the default), then proportions are fitted per group and regression coefficients are recalculated from those fits.
`bb_model`	Logical. Whether to perform the feature-level analysis using the beta-binomial model.
`prop_mode`	Optimization method used to estimate proportions. Possible value `"constrOptim"`.
`prop_tol`	The desired accuracy when estimating proportions.
`coef_mode`	Optimization method used to estimate regression coefficients. Possible value `"optim"`.
`coef_tol`	The desired accuracy when estimating regression coefficients.
`verbose`	Numeric. Definie the level of progress messages displayed. 0 - no messages, 1 - main messages, 2 - message for every gene fitting.
`BPPARAM`	Parallelization method used by `bplapply`.
`permutation_mode`	Character specifying which permutation scheme to apply for p-value calculation. When equal to `"all_genes"`, null distribution of p-values is calculated from all genes and the maximum number of permutation cycles is 10. When `permutation_mode = "per_gene"`, null distribution of p-values is calculated for each gene separately based on permutations of this individual gene. The latter approach may take a lot of computational time. We suggest using the first option.

One must specify one of the arguments: coef, design or contrast.

When contrast is used to define the null model, the null design matrix is recalculated using the same approach as in glmLRT function from edgeR.

Returns a dmDStest or dmSQTLtest object.

Malgorzata Nowicka

McCarthy, DJ, Chen, Y, Smyth, GK (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research 40, 4288-4297.

plotPValues glmLRT

# --------------------------------------------------------------------------
# Create dmDSdata object 
# --------------------------------------------------------------------------
## Get kallisto transcript counts from the 'PasillaTranscriptExpr' package

library(PasillaTranscriptExpr)

data_dir  <- system.file("extdata", package = "PasillaTranscriptExpr")

## Load metadata
pasilla_metadata <- read.table(file.path(data_dir, "metadata.txt"), 
header = TRUE, as.is = TRUE)

## Load counts
pasilla_counts <- read.table(file.path(data_dir, "counts.txt"), 
header = TRUE, as.is = TRUE)

## Create a pasilla_samples data frame
pasilla_samples <- data.frame(sample_id = pasilla_metadata$SampleName, 
  group = pasilla_metadata$condition)
levels(pasilla_samples$group)

## Create a dmDSdata object
d <- dmDSdata(counts = pasilla_counts, samples = pasilla_samples)

## Use a subset of genes, which is defined in the following file
gene_id_subset <- readLines(file.path(data_dir, "gene_id_subset.txt"))

d <- d[names(d) %in% gene_id_subset, ]

# --------------------------------------------------------------------------
# Differential transcript usage analysis - simple two group comparison 
# --------------------------------------------------------------------------

## Filtering
## Check what is the minimal number of replicates per condition 
table(samples(d)$group)

d <- dmFilter(d, min_samps_gene_expr = 7, min_samps_feature_expr = 3,
  min_gene_expr = 10, min_feature_expr = 10)

plotData(d)

## Create the design matrix
design_full <- model.matrix(~ group, data = samples(d))

## To make the analysis reproducible
set.seed(123)
## Calculate precision
d <- dmPrecision(d, design = design_full)

plotPrecision(d)

head(mean_expression(d))
common_precision(d)
head(genewise_precision(d))

## Fit full model proportions
d <- dmFit(d, design = design_full)

## Get fitted proportions
head(proportions(d))
## Get the DM regression coefficients (gene-level) 
head(coefficients(d))
## Get the BB regression coefficients (feature-level) 
head(coefficients(d), level = "feature")

## Fit null model proportions and perform the LR test to detect DTU
d <- dmTest(d, coef = "groupKD")

## Plot the gene-level p-values
plotPValues(d)

## Get the gene-level results
head(results(d))

## Plot feature proportions for a top DTU gene
res <- results(d)
res <- res[order(res$pvalue, decreasing = FALSE), ]

top_gene_id <- res$gene_id[1]

plotProportions(d, gene_id = top_gene_id, group_variable = "group")

plotProportions(d, gene_id = top_gene_id, group_variable = "group", 
  plot_type = "lineplot")

plotProportions(d, gene_id = top_gene_id, group_variable = "group", 
  plot_type = "ribbonplot")