Description Usage Arguments Details Author(s) Examples
This function allows easy import of results of different voting procedures for given combination of cohort/method/algorithm.
1 2 | votedEP(indexTable, votingType = "votingAlgoritm", method = "H3K4me1",
algorithm = "pearson", cohort = "Roadmap")
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indexTable |
an output of the makeIndexTable() for given combination of methods/algorithms/cohorts; a table should contain the following columns: path - paths to .rds files; methods - a method type used for the analysis: eg. H3K4me1; algorithms - algorithm used for the analysis: eg. dcor, cohorts - cohort used for the analysis: eg. Roadmap; type - define whether results are produced by voting, meta-analysis, from individual modelling or a result of regActivityAroundTSS() |
votingType |
"votingAlgoritm" (default; character) Describes which voting procedure was used to produce voting results. OPTIONS: ("votingAlgoritm","votingCohorts","votingMethods"). |
method |
"H3K4me1" (default; character). For which method to extract Enh~Promoter pairs. Common options: "H3K4me1","H3K27ac", "Methylation","DNase" |
algorithm |
"pearson" (default; character). For which algorithm to extract Enh~Promoter pairs. Common options:"pearson","spearman", "elasticnet","dcor","randomForest" |
cohort |
"Roadmap" (default; character). For which cohort to extract Enh~Promoter pairs. Common options:"Roadmap","Blueprint", "CEMT","McGill" |
This function allows easy import of results of different voting procedures for given combination of cohort/method/algorithm. For example, "votingAlgoritm" correspond to voting based on the results of pearson, spearman,elasticnet,dcor,randomForest modelling procedures for a combination of cohort and method (eg H3K4me1+Roadmap). In this case algorithm argument is ignored while importing "votingAlgoritm" results for H3K4me1+Roadmap
Inga Patarcic
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## Not run:
library(InteractionSet)
library(stringr)
IndexTable <- readRDS("/data/akalin/Projects/AAkalin_Catalog_RI/Results/Validation/Fishillevic/VoteD//CohortVoting_McGillH3K4me1.rds")
votedEP(indexTable,
votingType="votingAlgorithm",
method="H3K4me1",
algorithm="pearson",
cohort="Roadmap")
## End(Not run)
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