Performs an OverRepresentation Analysis (ORA) independently for each cluster of a time-course analysis, using as background (universe) all the proteins that were tested. It returns the combined results and a dotplot in which the size of each dot reflects the enrichment, the color its significance, and the number written inside the dot the count of proteins found in that geneset.
timecourse.enrichment(
DEprot.timecourse.object,
TERM2GENE,
clusters = NULL,
top.n = NULL,
universe = NULL,
gsub.pattern.prot.id = NULL,
min.cluster.size = 5,
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
pAdjustMethod = "BH",
dotplot.n = 5,
size.by = "FoldEnrichment",
size.range = c(5, 14),
number.size = 2.7,
show.numbers = TRUE,
max.term.length = 60,
viridis.option = "rocket"
)An object of class DEprot.timecourse.
Data.frame containing two columns 'gs_name' (IDs of the gene sets) and 'gene_symbol' (indicating the gene IDs). No default.
Numeric value (or vector) indicating the cluster(s) to analyze. Default: NULL (all the clusters).
Numeric value indicating how many best-ranked proteins of each cluster should be used for the enrichment. Default: NULL (all the proteins of the cluster).
Character vector indicating the background gene list. Default: NULL, meaning that all the proteins tested by analyze.timecourse are used. This is almost always the correct background for a proteomics experiment, since only the quantified proteins could have been detected as trending.
String indicating a pattern to be passed to gsub and to remove from the prot.id. Default: NULL (no changes in the IDs).
Numeric value indicating the minimal number of proteins required to run the enrichment on a cluster. Default: 5.
Numeric value indicating the adjusted pvalue cutoff on enrichment tests to report. Default: 0.05.
Numeric value indicating the qvalue cutoff on enrichment tests to report as significant. Default: 0.05.
String indicating the method to use for the p-value adjustment. One among "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". Default: "BH".
Numeric value indicating the maximum number of genesets displayed per cluster in the dotplot. Default: 5.
String indicating the metric mapped on the size of the dots. One among: 'FoldEnrichment' or 'GeneRatio'. Default: "FoldEnrichment".
Numeric vector of two elements indicating the minimal and maximal size of the dots. They must stay large enough for the numbers to fit inside. Default: c(5, 14).
Numeric value indicating the font size of the count displayed inside the dots. Default: 2.7.
Logic value indicating whether the number of proteins should be written inside the dots. Default: TRUE.
Numeric value indicating the maximal number of characters of the geneset names displayed on the y-axis (longer names are truncated). Default: 60.
String indicating the viridis palette used for the significance color scale. Default: "rocket".
An object of class DEprot.timecourse.enrichment.