xPierMatrix | R Documentation |
xPierMatrix
is supposed to extract priority matrix from a list
of pNode objects. Also supported is the aggregation of priority matrix
(similar to the meta-analysis) generating the priority results; we view
this functionality as the discovery mode of the prioritisation.
xPierMatrix(list_pNode, displayBy = c("score", "rank", "pvalue"), combineBy = c("intersect", "union"), aggregateBy = c("none", "fishers", "logistic", "Ztransform", "orderStatistic"), verbose = TRUE)
list_pNode |
a list of "pNode" objects |
displayBy |
which priority will be extracted. It can be "score" for priority score (by default), "rank" for priority rank, "pvalue" for priority p-value |
combineBy |
how to resolve nodes/targets from a list of "pNode" 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 |
If aggregateBy is 'none' (by default), a data frame containing priority matrix, with each column/predictor for either priority score, or priorty rank or priority p-value. If aggregateBy is not 'none', an object of the class "dTarget", a list with following components:
priority
: a data frame of nGene X 5 containing gene
priority (aggregated) information, where nGene is the number of genes,
and the 5 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 0-10 range)
predictor
: a data frame containing priority matrix, with
each column/predictor for either priority score, or priorty rank or
priority p-value
call
: the call that produced this result
none
xPierSNPs
## Not run: # Load the library library(Pi) ## End(Not run) RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev" ## Not run: df_score <- xPierMatrix(ls_pNode) ## End(Not run)