Plot p-values distribution

Share:

Description

Plot p-values distribution

Usage

1
2
3
4
5
6
7
plotTest(x, ...)

## S4 method for signature 'dmDStest'
plotTest(x, out_dir = NULL)

## S4 method for signature 'dmSQTLtest'
plotTest(x, out_dir = NULL)

Arguments

x

dmDStest or dmSQTLtest object.

...

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

out_dir

Character string that is used to save the plot in paste0(out_dir, plot_name, ".pdf") file. plot_name depends on type of a plot produced, for example, plot_name = "hist_features" for histogram with number of features per gene. If NULL, the plot is returned as ggplot object and can be further modified, for example, using theme().

Value

Plot a histogram of p-values.

Author(s)

Malgorzata Nowicka

See Also

data_dmDSdata, data_dmSQTLdata, plotData, plotDispersion, plotFit

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
###################################
### 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)