xPierCross: Function to extract priority matrix from a list of...

Description Usage Arguments Value Note See Also Examples

View source: R/xPierCross.r

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
xPierCross(
list_xTarget,
displayBy = c("rating", "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",
guid = NULL
)

Arguments

list_xTarget

a list of "dTarget"/"sTarget" objects or a "dTarget"/"sTarget" object

displayBy

which priority will be extracted. It can be "rating" for priority score/rating (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

guid

a valid (5-character) Global Unique IDentifier for an OSF project. 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/rating, or priorty rank or priority p-value. If aggregateBy is not 'none', an object of the class "cTarget", a list with following components:

Note

none

See Also

xSymbol2GeneID

Examples

1
2
3
4
5
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
df_score <- xPierCross(ls_xTarget)

## End(Not run)

Pi documentation built on Nov. 29, 2021, 3 p.m.