Aberrant Expression

Datasets: all

Gene annotations: v29

Summaries

Counts summary

Gene annotation version v29

• all

OUTRIDER summary

Gene annotation version v29

• all

Files

• /s/project/drop-analysis/processed_results/aberrant_expression/v29/outrider/all/ods.Rds

• /s/project/drop-analysis/processed_results/aberrant_expression/v29/outrider/all/OUTRIDER_results.tsv

Analyze Individual Results

Display the results table of the first dataset

Choose a random gene and sample to plot. Outliers are in red.

gene <- ifelse(nrow(res)>1, res[1, geneID], rownames(ods)[1])
sample <- ifelse(nrow(res)>1, res[1, sampleID], colnames(ods)[1])

Volcano plot

setting basePlot = FALSE creates an interactive plot that allows finding the gene(s) of interest

OUTRIDER::plotVolcano(ods, sample, basePlot = TRUE,
                      zScoreCutoff = snakemake@config$aberrantExpression$zScoreCutoff,
                      padjCutoff = snakemake@config$aberrantExpression$padjCutoff)

Gene expression plot (normalized counts)

OUTRIDER::plotExpressionRank(ods, gene, basePlot = TRUE,
                      zScoreCutoff = snakemake@config$aberrantExpression$zScoreCutoff,
                      padjCutoff = snakemake@config$aberrantExpression$padjCutoff)

Expected vs observed counts

OUTRIDER::plotExpectedVsObservedCounts(ods, gene, basePlot = TRUE)