DRIMSeq (version 1.0.2)

dmDSfit-class: dmDSfit object

Description

dmDSfit extends the dmDSdispersion class by adding the full model Dirichlet-multinomial feature proportion estimates needed for the differential splicing analysis. Feature ratios are estimated for each gene and each condition. Result of dmFit.

Usage

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

Arguments

x

dmDSdispersion object.

...

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

Value

• proportions(x): Get a data frame with estimated feature ratios for each condition.
• statistics(x): Get a data frame with maximum log-likelihoods for each condition.

Slots

dispersion

Character specifying which type of dispersion was used for fitting: "common_dispersion" or "genewise_dispersion".

fit_full

MatrixList containing the per gene feature ratios. Columns correspond to different conditions. Additionally, the full model likelihoods are stored in metadata slot.

See Also

data_dmDSdata, dmDSdata, dmDSdispersion, dmDStest

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::SrialParam())

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