directExplorer2d {directPA}

Batch Direction Analysis in 2-dimentional space

Description

Rotate to the direction of interest in polar coordinates by degree (e.g. pi/4).

Usage

directExplorer2d(Tc, annotation=NULL, gene.method="OSP", 
path.method="Stouffer", top=10, nd=8, ...)

Arguments

Tc

a numeric matrix with 2 columns. The rows are genes or phosphorylation sites and the columns are treatments vs control statistics.

annotation

a list with names correspond to pathways or kinases and elements correspond to genes or substrates belong to each pathway or kinase, respectively.

gene.method

the method to be used for integrating statistics across treatments for each gene or phosphorylation site. Available methods are Stouffer, OSP, Fisher, and maxP. Default method is OSP.

path.method

the method to be used for integrating statistics of all genes or phosphorylation sites that belongs to a pathway or kinase. Available methods are Stouffer, OSP, Fisher, and maxP. Default method is Stouffer.

top

the number of entries to be highlighted in the plot.

nd

the number of directions to plot (4 or 8)

...

parameters for controlling the plot.

Value

The the list of enrichment analysis in tables.

Examples

# load the phosphoproteomics dataset
data(HEK)

# load the kinase-substrate annoations
data(PhosphoSite)

# test enrichment on 8 directions in polar coordinate system.
bda <- directExplorer2d(Tc=HEK, annotation=PhosphoSite.mouse)

# the direction are denoted as follow for the two treatments vs control:
# ++: up-regulated in both treatments
# +*: up-regulated in the first treatment and unchanged in the second treatment
# +-: up-regulated in the first treatment and down-regulated in the second treatment
# *-: unchanged in the first treatment and down-regulated in the second treatment
# --: down-regulated in both treatments
# -*: down-regulated in the first treatment and unchanged in the second treatment
# -+: down-regulated in the first treatment and up-regulated in the second treatment
# *+: unchanged in the first treatment and up-regulated in the second treatment

# sort the most enriched phosphorylation sites and kinases on down-regulaiton from both 
# treatments (i.e. "--") and displa the top-10 entries
bda$gene.tab[order(bda$gene.tab[,"--"]),][1:10,]
bda$path.tab[order(bda$path.tab[,"--"]),][1:10,]