infoSource: Get summary statistics on graphs and variables

Description Usage Arguments Value Note Examples

View source: R/mainFunctions.R

Description

The infoSource function provides a summary of the results by focusing on either variables or graphs.

Usage

1
infoSource(sourceObj, map.name.variable = NULL, method = "fdr")

Arguments

sourceObj

a SourceSetObj object, i.e. the output of the sourceSet function

map.name.variable

a list of customized labels to be associated with the names of the genes. Each list element must contain only one value (i.e. the new label), and the name of each element must be associated with the names of the genes given as input to the sourceSet function (column names of data input argument). If a label is not mapped, the original name is used

method

correction method for p-values calculated on graphs. The adjustment methods allowed are: fdr (default), holm, hochberg, hommel, bonferroni, BH, BY or none. For more details refer to p.adjust.

Value

The function guides the user in identifying interesting variables returning two objects:

Note

Ideally, variables of the primary dysregulation will be elements of the source set in all input graphs that contain them and will thus have high values of source.impact and score. However, if a given variable appears in a single graph, and belongs to its source set, these indices can be deceptive.

For this reason, relevance serves to identify variables that apart from being good candidates for primary genes, also appear frequently in the input graphs. Which index is to be preferred depends on the objective of the analysis: in case of exploratory analysis, we suggest to rely on relevance.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
## Load the SourceSetObj obtained from the source set analysis of ALL dataset

# see vignette for more details
print(load(file=system.file("extdata","ALLsourceresult.RData",package = "SourceSet")))
class(results.all)

info.all<-infoSource(sourceObj = results.all)
## results of individual input graphs
info.all$graph

## results of individual variables
# ..that appear in more than one graph and with relevance>0
info.all.genes<-info.all$variable[info.all$variable$n.graph>1 & info.all$variable$relevance>0,]
# ..ordered by score
ind.ord<-order(info.all.genes$relevance,decreasing = TRUE)
info.all.genes[ind.ord,]

SourceSet documentation built on Oct. 30, 2019, 9:38 a.m.