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

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## S4 method for signature 'dmDStest'
proportions(x)

## S4 method for signature 'dmDStest'
statistics(x)

results(x, ...)

## S4 method for signature 'dmDStest'
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.

Author(s)

Malgorzata Nowicka

See Also

data_dmDSdata, dmDSdata, dmDSdispersion, dmDSfit

Examples

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###################################
### 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))