xPierCross | R Documentation

## Function to extract priority matrix from a list of dTarget/sTarget objects

### Description

`xPierCross` is supposed to extract priority matrix from a list of dTarget objects. Also supported is the aggregation of priority matrix (similar to the meta-analysis) generating the priority results; we view this functionality as the cross mode of the prioritisation.

### Usage

    xPierCross(list_xTarget, displayBy = c("priority", "rank", "pvalue",
    "fdr"), combineBy = c("intersect", "union"), aggregateBy = c("none",
    "fishers", "logistic", "Ztransform", "orderStatistic"), verbose = TRUE,
    RData.location = "http://galahad.well.ox.ac.uk/bigdata")

### Arguments

`list_xTarget` | a list of "dTarget"/"sTarget" objects or a "dTarget"/"sTarget" object
`displayBy` | which priority will be extracted. It can be "priority" for priority score (by default), "rank" for priority rank, "pvalue" for priority p-value, "fdr" for priority fdr
`combineBy` | how to resolve nodes/targets from a list of "dTarget"/"sTarget" objects. It can be "intersect" for intersecting nodes (by default), "union" for unionising nodes
`aggregateBy` | the aggregate method used. It can be either "none" for no aggregation, or "orderStatistic" for the method based on the order statistics of p-values, "fishers" for Fisher's method, "Ztransform" for Z-transform method, "logistic" for the logistic method. Without loss of generality, the Z-transform method does well in problems where evidence against the combined null is spread widely (equal footings) or when the total evidence is weak; Fisher's method does best in problems where the evidence is concentrated in a relatively small fraction of the individual tests or when the evidence is at least moderately strong; the logistic method provides a compromise between these two. Notably, the aggregate methods 'fishers' and 'logistic' are preferred here
`verbose` | logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display
`RData.location` | the characters to tell the location of built-in RData files. See `xRDataLoader` for details

### Value

If aggregateBy is 'none' (by default), a data frame containing priority matrix, with each column/disease for either priority score, or priorty rank or priority p-value. If aggregateBy is not 'none', an object of the class "cTarget", a list with following components:

- `priority`: a data frame of nGene X 6 containing gene priority (aggregated) information, where nGene is the number of genes, and the 6 columns are "name" (gene names), "rank" (ranks of the priority scores), "pvalue" (the aggregated p-value, converted from empirical cumulative distribution of the probability of being GSP), "fdr" (fdr adjusted from the aggregated p-value), "priority" (-log10(pvalue) but rescaled into the 5-star ratings), "description" (gene description)

- `disease`: a data frame containing disease matrix, with each column/disease for either priority score, or priorty rank or priority p-value

### Note

none

### See Also

`xPierMatrix`

### Examples

    ## Not run:
    # Load the library
    library(Pi)

    ## End(Not run)
    RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
    ## Not run:
    df_score <- xPierCross(ls_xTarget)

    ## End(Not run)