visGSEA

eTerm

which sample will be used. It can be
index or sample names

which_sample

which term will be used. It can be
index or term ID or term names

which_term

type of score weigth. It can be "0" for
unweighted (an equivalent to Kolmogorov-Smirnov, only
considering the rank), "1" for weighted by input gene
score (by default), and "2" for over-weighted, and so on

weight

the orientation of the plots. It can
be either "vertical" (default) or "horizontal"

orientation

logical to indicate whether to open a new
page. By default, it sets to true for opening a new page

newpage

<code>visGSEA</code> is supposed to visualise running enrichment
score for a given sample and a gene set. To help understand
the underlying running enrichment score, the input gene
scores are also displayed. Positions for members in the
given gene set are color-coded in both displays (red line
for the positive gene scores, and green line for the
negative).

The 'dnet' package is initiated to fill in the need of an open-source tool for digitised data in an integrative manner. More specifically, dnet intends to analyse the biological network whose nodes/genes are associated with digitised information such as expression levels across samples. To help make sense of identified networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific age information in major organisms including human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. In summary, dnet aims to deliver an eye-intuitive tool with rich visuals but less inputs.

visGSEA: Function to visualise running enrichment score for a given sample and a gene set

Description

Usage

Arguments

Value

See Also

Examples