xPierMatrix | R Documentation |
xPierMatrix
is supposed to extract priority or evidence 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", "weight", "pvalue", "evidence"), combineBy = c("union", "intersect"), aggregateBy = c("none", "fishers", "logistic", "Ztransform", "orderStatistic"), verbose = TRUE, RData.location = "http://galahad.well.ox.ac.uk/bigdata")
list_pNode |
a list of "pNode" objects or a "pNode" object |
displayBy |
which priority will be extracted. It can be "score" for priority score (by default), "rank" for priority rank, "weight" for seed weight, "pvalue" for priority p-value, "evidence" for the evidence (seed info) |
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 |
RData.location |
the characters to tell the location of built-in
RData files. See |
If displayBy is 'evidence', an object of the class "eTarget", a list with following components:
evidence
: a data frame of nGene X 6 containing gene
evidence information, where nGene is the number of genes, and the 7
columns are seed info including "Overall" for the number of different
types of seeds, followed by details on individual type of seeds (that
is, "OMIM", "Phenotype", "Function", "nearbyGenes", "eQTL", "HiC")
metag
: an "igraph" object
Otherwise (if displayBy is not 'evidence'), 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 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) and seed info including "Overall" for the number of
different types of seeds, followed by details on individual type of
seeds (that is, "OMIM", "Phenotype", "Function", "nearbyGenes", "eQTL",
"HiC")
predictor
: a data frame containing predictor matrix, with
each column/predictor for either priority score, or priorty rank or
priority p-value
metag
: an "igraph" object
none
xPierSNPsAdv
## Not run: # Load the library library(Pi) ## End(Not run) RData.location <- "http://galahad.well.ox.ac.uk/bigdata" ## Not run: # get predictor matrix for targets df_score <- xPierMatrix(ls_pNode) # get evidence for targets eTarget <- xPierMatrix(ls_pNode, displayBy="evidence") # get target priority in a discovery mode dTarget <- xPierMatrix(ls_pNode, displayBy="pvalue", aggregateBy="fishers") ## End(Not run)