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

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

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("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:

• 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

xSymbol2GeneID

Examples

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.