geneSetsStats {sparrow}R Documentation

Summarizes useful statistics per gene set from a SparrowResult

Description

This function calculates the number of genes that move up/down for the given contrasts, as well as mean and trimmed mean of the logFC and t-statistics. Note that the statistics calculated and returned here are purely a function of the statistics generated at the gene-level stage of the analysis.

Usage

geneSetsStats(
  x,
  feature.min.logFC = 1,
  feature.max.padj = 0.1,
  trim = 0.1,
  reannotate.significance = FALSE,
  as.dt = FALSE
)

Arguments

x

A SparrowResult object

feature.min.logFC

used with feature.max.padj to identify the individual features that are to be considered differentially expressed.

feature.max.padj

used with feature.min.logFC to identify the individual features that are to be considered differentially expressed.

trim

The amount to trim when calculated trimmed t and logFC statistics for each geneset.

reannotate.significance

this is internally by the package, and should left as FALSE when used by the user.

as.dt

If FALSE (default), the data.frame like thing that this funciton returns will be set to a data.frame. Set this to TRUE to keep this object as a data.table

Value

A data.table with statistics at the gene set level across the prescribed contrast run on x. These statistics are independent of any particular GSEA method, but rather summarize aggregate shifts of the gene sets individual features. The columns included in the output are summarized below:

Examples

vm <- exampleExpressionSet(do.voom=TRUE)
gdb <- exampleGeneSetDb()
mg <- seas(vm, gdb, design = vm$design, contrast = 'tumor')
head(geneSetsStats(mg))

[Package sparrow version 1.0.1 Index]