DRIMSeq (version 1.0.2)

dmDStest-class: dmDStest object

Description

dmDStest extends the dmDSfit class by adding the null model Dirichlet-multinomial feature proportion estimates and the results of testing for differential splicing. Proportions are calculated for each gene from pooled (no grouping into conditions) counts. Result of dmTest.

Usage

"proportions"(x)
"statistics"(x)
results(x, ...)
"results"(x)

Arguments

x

dmDStest object.

...

Other parameters that can be defined by methods using this generic.

Value

• proportions(x): Get a data frame with estimated feature ratios for full model and null models specified in dmTest with compared_groups parameter.
• statistics(x): Get a data frame with full and null log-likelihoods and degrees of freedom.
• results(x): Get a data frame with results. See Slots.

Slots

compared_groups

Character vector specifying which groups/conditions should be compared. By default, the comparison is done among all the groups specified by group column in samples(x).

fit_null

MatrixList. Contains null proportions, likelihoods and degrees of freedom for a comparison specified with compared_groups.

results

Data frame with gene_id - gene IDs, lr - likelihood ratio statistics, df - degrees of freedom, pvalue - p-values and adj_pvalue - Benjamini & Hochberg adjusted p-values for comparison specified in compared_groups.

See Also

data_dmDSdata, dmDSdata, dmDSdispersion, dmDSfit

Examples

###################################
### Differential splicing analysis
###################################
# If possible, use BPPARAM = BiocParallel::MulticoreParam() with more workers

d <- data_dmDSdata

### 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_samps_feature_prop = 0)

### Calculate dispersion
d <- dmDispersion(d, BPPARAM = BiocParallel::SerialParam())
### Fit full model proportions 
d <- dmFit(d, BPPARAM = BiocParallel::SerialParam())

### Fit null model proportions and test for DS 
d <- dmTest(d, BPPARAM = BiocParallel::SerialParam()) 
plotTest(d)

head(proportions(d)) 
head(statistics(d)) 
head(results(d))