DRIMSeq (version 1.0.2)

dmSQTLtest-class: dmSQTLtest object

Description

dmSQTLtest extends the dmSQTLfit class by adding the null model Dirichlet-multinomial feature proportion estimates and the results of testing for sQTLs. Proportions are calculated for each gene-block pair from pooled (no grouping into conditions) counts. Result of dmTest.

Usage

"results"(x)

Arguments

x

dmSQTLtest object.

...

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

Value

• results(x): Get a data frame with results. See Slots.

Slots

fit_null

List of MatrixList. Each of them contains null proportions, likelihoods and degrees of freedom for all the blocks (unique SNPs) assigned to a given gene.

results

Data frame with gene_id - gene IDs, block_id - block IDs, snp_id - SNP IDs, lr - likelihood ratio statistics, df - degrees of freedom, pvalue - p-values and adj_pvalue - Benjamini & Hochberg adjusted p-values.

See Also

data_dmSQTLdata, dmSQTLdata, dmSQTLdispersion, dmSQTLfit

Examples

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

d <- data_dmSQTLdata

### Filtering
d <- dmFilter(d, min_samps_gene_expr = 70, min_samps_feature_expr = 5, 
   min_samps_feature_prop = 0, minor_allele_freq = 5, 
   BPPARAM = BiocParallel::SerialParam())

### 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 sQTLs
d <- dmTest(d, BPPARAM = BiocParallel::SerialParam())
plotTest(d)

head(results(d))