gseaFingerprint: Extract pathway fingerprints from GSEA results

In bedapub/ribiosGSEA: Gene-Set Enrichment Analysis Tools in Ribios

Extract pathway fingerprints from GSEA results

Description

gseaFingerprint extracts pathway fingerprints from the result of one GSEA result. gseaFingerprintMatrix extracts multiple signatures and organizes into the form of rectangular matrix.

Usage

gseaFingerprint(
  gseaDir,
  value = c("q", "es", "nes"),
  threshold = 1e-04,
  sortByName = TRUE
)

gseaFingerprintMatrix(gseaDirs, value = c("q", "es", "nes"), ...)

Arguments

gseaDir	Character, a GSEA output directory. Notice the directory must be accessible by the R session. A common mistake is to use a relative path which cannot be found.
value	Character, the statistic to extract, currently supporting q, es and nes
threshold	Numeric, minimum threshold of q-value, passed to gseaQvalue
sortByName	Logical, whether signatures should be sorted by name
gseaDirs	Character vector, GSEA output directories
...	Parameters passed to gseaFingerprint by gseaFingerprintMatrix

Details

gseaFingerprint extracts pathway signature from one GSEA output directory. While gseaFingerprintMatrix simultaneously extracts from more than one GSEA output directories, and organizes pathway signatures in a rectangular matrix form.

gseaFingerprintMatrix takes care of signature mapping between different GSEA result sets.

Value

gseaFingerprint returns a data.frame with two columns name and value, recording gene signature (pathway) names and the statistic chosen by the user.

gseaFingerprintMatrix returns a matrix, with the union set of gene signatures from all GSEA output result sets as rows, and GSEA result names as columns.

Author(s)

Jitao David Zhang <[e-mail]>

See Also

See gseaQvalue and gseaES for how to choose the statistic to produce pathway signatures.

Examples

gseaDirZip <- system.file(package="ribiosGSEA","extdata/gseaDirs.zip")
tmpDir <- tempdir()
utils::unzip(gseaDirZip, exdir=tmpDir)
gseaDir <- file.path(tmpDir, "gseaDirs")
gseaDirs <- dir(gseaDir, full.names=TRUE)
gseaFp <- gseaFingerprint(gseaDirs[1], value="q")
gseaFps <- gseaFingerprintMatrix(gseaDirs, value="q")

bedapub/ribiosGSEA documentation built on March 30, 2023, 3:26 p.m.