kinasePA {directPA}

Direction Analysis for Kinases

Description

This is a wrapper for runing directPA for kinase perturbation analysis (kinasePA)

Usage

kinasePA(Tc, direction, annotation, minSize=5, substrate.method="OSP", 
kinase.method="Stouffer", visualize=TRUE, ...)

Arguments

Tc

a numeric matrix. The columns are phosphorylation sites and the columns are treatments vs control statistics.

direction

the direction to be tested for enrichment. Either specified as a degree for two-dimensional analysis or as contrast (in a triplet) for three-dimensional analysis.

annotation

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

minSize

the size of annotation groups to be considered for calculating enrichment. Groups that are smaller than the minSize will be removed from the analysis.

substrate.method

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

kinase.method

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

visualize

whether to visualize the plot.

...

other visualization parameters to pass on.

Value

a list that contains directional p-values for each substrate and directional enrichment for each kinase.

Examples

# load the phosphoproteomics dataset
data(HEK)

# load the kinase-substrate annoations
data(PhosphoSite)

# direction pathway analysis in 2-dimensional space. Implemented as rotating by degree 
# (1) test combined effect of Torin1 and Rapamycin vs insul both on "down-regulation"
# (180 degree to original direction)
kPA <- kinasePA(Tc=HEK, direction=pi, annotation=PhosphoSite.mouse)
kPA$kinase[order(unlist(kPA$kinase[,1])),][1:20,]
# rank substrates on the direciton of interest
sort(kPA$substrate.pvalues)[1:20]

# (2) test combined effect of Torin1 and Rapamycin vs insul on "no change and down-regulation"
# (135 degree to the original direction) 
kPA <- kinasePA(Tc=HEK, direction=pi*3/4, annotation=PhosphoSite.mouse)
kPA$kinase[order(unlist(kPA$kinase[,1])),][1:20,]

# (3) test combined effect of Torin1 and Rapamycin vs insul on "down-regulation and no change"
# (225 degree to the original direction) 
kPA <- kinasePA(Tc=HEK, direction=pi*5/4, annotation=PhosphoSite.mouse)
kPA$kinase[order(unlist(kPA$kinase[,1])),][1:20,]