Aberrant Splicing

Datasets: all

Gene annotations: v29

Summaries

Counts summary

• all

FRASER summary

Gene annotation version v29

• all

Files

• /s/project/drop-analysis/processed_results/aberrant_splicing/datasets/savedObjects/all–v29/fds-object.RDS

• /s/project/drop-analysis/processed_results/aberrant_splicing/results/v29/fraser/all/results_per_junction.tsv

Analyze individual results

# Read the first fds object and results table
fds <- loadFraserDataSet(file = snakemake@input$fds_files[[1]])
res <- fread(snakemake@input$result_tables[[1]])

Display the results table of the first dataset

Get a splice site and sample of interest. Outliers are in red.

sample <- ifelse(nrow(res)>1, res[1, sampleID], colnames(fds)[1])
siteIndex <- 4

Get asplice metric of interest. Choose any of the ones that have been fitted Here we use the splice metric of the first outlier in the results table

splice_metric <- res[1, type]

Volcano plot

# set basePlot to FALSE to create an interactive plot
FRASER::plotVolcano(fds, sample, type = splice_metric, basePlot = TRUE,
                    deltaPsiCutoff = snakemake@config$aberrantSplicing$deltaPsiCutoff,
                    padjCutoff = snakemake@config$aberrantSplicing$padjCutoff)

Expression plot

FRASER::plotExpression(fds, type = splice_metric, idx = siteIndex, basePlot = TRUE)

Expected vs observed PSI (or theta)

FRASER::plotExpectedVsObservedPsi(fds, type = splice_metric,
                                  idx = siteIndex, basePlot = TRUE)